[Samsung Galaxy Nexus] Cjmx:
I'm having the same issues, it seems to be a problem with the aapt binary.

The Gingerbread aapt gave this error:

X:\android\crt>apktool b -f framework-res
W: Could not find sources
I: Building resources...
invalid resource directory name: X:\android\crt\framework-res\res/drawable-sw600
dp-hdpi
invalid resource directory name: X:\android\crt\framework-res\res/layout-sw600dp

invalid resource directory name: X:\android\crt\framework-res\res/layout-w600dp
invalid resource directory name: X:\android\crt\framework-res\res/values-h720dp
invalid resource directory name: X:\android\crt\framework-res\res/values-sw600dp

invalid resource directory name: X:\android\crt\framework-res\res/values-sw600dp
-land
invalid resource directory name: X:\android\crt\framework-res\res/values-sw600dp
-w1024dp
invalid resource directory name: X:\android\crt\framework-res\res/values-sw600dp
-w1280dp
invalid resource directory name: X:\android\crt\framework-res\res/values-w360dp
invalid resource directory name: X:\android\crt\framework-res\res/values-w480dp
invalid resource directory name: X:\android\crt\framework-res\res/values-w500dp
invalid resource directory name: X:\android\crt\framework-res\res/values-w600dp
invalid resource directory name: X:\android\crt\framework-res\res/values-w720dp
Exception in thread "main" brut.androlib.AndrolibException: brut.common.BrutExce
ption: could not exec command: [aapt, p, -F, C:\Users\Cj\AppData\Local\Temp\APKT
OOL6979654477300252838.tmp, -x, -S, X:\android\crt\framework-res\res, -M, X:\and
roid\crt\framework-res\AndroidManifest.xml]
at brut.androlib.res.AndrolibResources.aaptPackage(AndrolibResources.jav
a:193)
at brut.androlib.Androlib.buildResourcesFull(Androlib.java:301)
at brut.androlib.Androlib.buildResources(Androlib.java:248)
at brut.androlib.Androlib.build(Androlib.java:171)
at brut.androlib.Androlib.build(Androlib.java:154)
at brut.apktool.Main.cmdBuild(Main.java:182)
at brut.apktool.Main.main(Main.java:67)
Caused by: brut.common.BrutException: could not exec command: [aapt, p, -F, C:\U
sers\Cj\AppData\Local\Temp\APKTOOL6979654477300252838.tmp, -x, -S, X:\android\cr
t\framework-res\res, -M, X:\android\crt\framework-res\AndroidManifest.xml]
at brut.util.OS.exec(OS.java:83)
at brut.androlib.res.AndrolibResources.aaptPackage(AndrolibResources.jav
a:191)
... 6 more

The ICS aapt, same framework to recompile(4.0.3), now gives this:

X:\android\crt>apktool b -f framework-res
W: Could not find sources
I: Building resources...
X:\android\crt\framework-res\res\values\plurals.xml:79: error: Multiple substitu
tions specified in non-positional format; did you mean to add the formatted="fal
se" attribute?
X:\android\crt\framework-res\res\values\plurals.xml:79: error: Found tag </item>
where </plurals> is expected
X:\android\crt\framework-res\res\values-af\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-af\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-am\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-am\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-ar\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-ar\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-bg\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-bg\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-ca\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-ca\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-cs\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-cs\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-da\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-da\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-de\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-de\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-el\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-el\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-en-rGB\plurals.xml:79: error: Multiple s
ubstitutions specified in non-positional format; did you mean to add the formatt
ed="false" attribute?
X:\android\crt\framework-res\res\values-en-rGB\plurals.xml:79: error: Found tag
</item> where </plurals> is expected
X:\android\crt\framework-res\res\values-es\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-es\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-es-rUS\plurals.xml:79: error: Multiple s
ubstitutions specified in non-positional format; did you mean to add the formatt
ed="false" attribute?
X:\android\crt\framework-res\res\values-es-rUS\plurals.xml:79: error: Found tag
</item> where </plurals> is expected
X:\android\crt\framework-res\res\values-fa\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-fa\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-fi\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-fi\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-fr\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-fr\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-hi\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-hi\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-hr\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-hr\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-hu\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-hu\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-in\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-in\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-it\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-it\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-iw\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-iw\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-ja\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-ja\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-ko\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-ko\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-lt\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-lt\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-lv\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-lv\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-ms\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-ms\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-nb\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-nb\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-nl\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-nl\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-pl\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-pl\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-pt\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-pt\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-pt-rPT\plurals.xml:79: error: Multiple s
ubstitutions specified in non-positional format; did you mean to add the formatt
ed="false" attribute?
X:\android\crt\framework-res\res\values-pt-rPT\plurals.xml:79: error: Found tag
</item> where </plurals> is expected
X:\android\crt\framework-res\res\values-ro\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-ro\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-ru\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-ru\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-sk\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-sk\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-sl\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-sl\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-sr\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-sr\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-sv\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-sv\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-sw\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-sw\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-th\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-th\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-tl\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-tl\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-tr\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-tr\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-uk\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-uk\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-vi\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-vi\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
X:\android\crt\framework-res\res\values-zh-rCN\plurals.xml:79: error: Multiple s
ubstitutions specified in non-positional format; did you mean to add the formatt
ed="false" attribute?
X:\android\crt\framework-res\res\values-zh-rCN\plurals.xml:79: error: Found tag
</item> where </plurals> is expected
X:\android\crt\framework-res\res\values-zh-rTW\plurals.xml:79: error: Multiple s
ubstitutions specified in non-positional format; did you mean to add the formatt
ed="false" attribute?
X:\android\crt\framework-res\res\values-zh-rTW\plurals.xml:79: error: Found tag
</item> where </plurals> is expected
X:\android\crt\framework-res\res\values-zu\plurals.xml:79: error: Multiple subst
itutions specified in non-positional format; did you mean to add the formatted="
false" attribute?
X:\android\crt\framework-res\res\values-zu\plurals.xml:79: error: Found tag </it
em> where </plurals> is expected
Exception in thread "main" brut.androlib.AndrolibException: brut.common.BrutExce
ption: could not exec command: [aapt, p, -F, C:\Users\Cj\AppData\Local\Temp\APKT
OOL5397850870725338747.tmp, -x, -S, X:\android\crt\framework-res\res, -M, X:\and
roid\crt\framework-res\AndroidManifest.xml]
at brut.androlib.res.AndrolibResources.aaptPackage(AndrolibResources.jav
a:193)
at brut.androlib.Androlib.buildResourcesFull(Androlib.java:301)
at brut.androlib.Androlib.buildResources(Androlib.java:248)
at brut.androlib.Androlib.build(Androlib.java:171)
at brut.androlib.Androlib.build(Androlib.java:154)
at brut.apktool.Main.cmdBuild(Main.java:182)
at brut.apktool.Main.main(Main.java:67)
Caused by: brut.common.BrutException: could not exec command: [aapt, p, -F, C:\U
sers\Cj\AppData\Local\Temp\APKTOOL5397850870725338747.tmp, -x, -S, X:\android\cr
t\framework-res\res, -M, X:\android\crt\framework-res\AndroidManifest.xml]
at brut.util.OS.exec(OS.java:83)
at brut.androlib.res.AndrolibResources.aaptPackage(AndrolibResources.jav
a:191)
... 6 more

I think the guys at apktools are working on it according to these posts (sorry, cant post links yet):

code.google.com/p/android-apktool/issues/detail?id=267

code.google.com/p/android-apktool/issues/detail?id=277

EDIT: did more research and found the solution, in case anybody needs it, I've attached an apktool version that will work with ICS

Found here:

xdaforums.com/showpost.php?p=22070364&postcount=6