[Android Themes] cavarr:
In AutoAPKTool2.0.3d I I have this same problem when recompile:

[*] _INPUT_APK\framework-res.apk
decompiling _INPUT_APK\framework-res.apk...
I: Loading resource table...
I: Loaded.
I: Decoding file-resources...
I: Decoding values*/* XMLs...
I: Done.
I: Copying assets and libs...
[*] _INPUT_APK\SystemUI.apk
decompiling _INPUT_APK\SystemUI.apk...
I: Baksmaling...
I: Loading resource table...
I: Loaded.
I: Loading resource table from file: C:\Windows\system32\config\systemprofile\apktool\framework\1.apk
I: Loaded.
I: Decoding file-resources...
I: Decoding values*/* XMLs...
I: Done.
I: Copying assets and libs...

[*] framework-res folder
recompiling framework-res.apk...
W: Could not find sources
I: Building resources...
I: Building apk file...
Nie moľna odnale«† dysku.
[*] SystemUI folder
recompiling SystemUI.apk...
I: Smaling...
I: Building resources...
W/asset ( 1976): Asset path C:\Windows\system32\config\systemprofile\apktool\framework\1.apk is neither a directory nor file (type=1).
ERROR: Asset package include 'C:\Windows\system32\config\systemprofile\apktool\framework\1.apk' not found.
Exception in thread "main" brut.androlib.AndrolibException: brut.common.BrutException: could not exec command: [aapt, p, -F, C:\Users\root\AppData\Local\Temp\APKTOOL3964029022067530029.tmp, -I, C:\Windows\system32\config\systemprofile\apktool\framework\1.apk, -S, C:\ICS\AutoAPKTool2.0.3d\AutoAPKTool2.0.3d\_INPUT_APK\SystemUI\res, -M, C:\ICS\AutoAPKTool2.0.3d\AutoAPKTool2.0.3d\_INPUT_APK\SystemUI\AndroidManifest.xml]
at brut.androlib.res.AndrolibResources.aaptPackage(Unknown Source)
at brut.androlib.Androlib.buildResourcesFull(Unknown Source)
at brut.androlib.Androlib.buildResources(Unknown Source)
at brut.androlib.Androlib.build(Unknown Source)
at brut.androlib.Androlib.build(Unknown Source)
at brut.apktool.Main.cmdBuild(Unknown Source)
at brut.apktool.Main.main(Unknown Source)
Caused by: brut.common.BrutException: could not exec command: [aapt, p, -F, C:\Users\root\AppData\Local\Temp\APKTOOL3964029022067530029.tmp, -I, C:\Windows\system32\config\systemprofile\apktool\framework\1.apk, -S, C:\ICS\AutoAPKTool2.0.3d\AutoAPKTool2.0.3d\_INPUT_APK\SystemUI\res, -M, C:\ICS\AutoAPKTool2.0.3d\AutoAPKTool2.0.3d\_INPUT_APK\SystemUI\AndroidManifest.xml]
at brut.util.OS.exec(Unknown Source)
... 7 more
Nie moľna odnale«† dysku.

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2011-11-04 -- 17:06:39,63
--------------------------------------------------------------
java version "1.7.0"
Java(TM) SE Runtime Environment (build 1.7.0-b147)
Java HotSpot(TM) 64-Bit Server VM (build 21.0-b17, mixed mode)
I: Framework installed to: C:\Windows\system32\config\systemprofile\apktool\framework\1.apk
Nazwa 'else' nie jest rozpoznawana jako polecenie wewn©trzne lub zewn©trzne,
program wykonywalny lub plik wsadowy.
Nazwa 'else' nie jest rozpoznawana jako polecenie wewn©trzne lub zewn©trzne,
program wykonywalny lub plik wsadowy.
Nazwa 'else' nie jest rozpoznawana jako polecenie wewn©trzne lub zewn©trzne,
program wykonywalny lub plik wsadowy.
--------------------------------------------------------------
2011-11-04 -- 17:54:24,20
--------------------------------------------------------------
java version "1.7.0"
Java(TM) SE Runtime Environment (build 1.7.0-b147)
Java HotSpot(TM) 64-Bit Server VM (build 21.0-b17, mixed mode)
I: Framework installed to: C:\Windows\system32\config\systemprofile\apktool\framework\1.apk

Im must recompile app or only bulid usable apk?