[Android Software/Hacking General [Developers Only]] x_one:
FXP isn't stock, it's unofficial build of CM for Xperia ( http://freexperiaproject.com ).

Here is the log. I've got the same errors when I was using autopatcher script without gui.

ROOT= /cygdrive/d/Janusz/AutoPatcher/ApGPackages/ap
TOOL= /cygdrive/d/Janusz/AutoPatcher/ApGPackages/ap/patch_tools.tgz
ROM= /cygdrive/d/Janusz/AutoPatcher/FXP210_cm-10-20130309-UNOFFICIAL-haida_x01.zip
ROMX= D:\Janusz\AUTOPA~1\FXP210~4.ZIP

### verify tools ###
/cygdrive/d/Janusz/AutoPatcher/ApGPackages/cygwin/bin/patch
/cygdrive/d/Janusz/AutoPatcher/ApGPackages/cygwin/bin/tar
/cygdrive/d/Janusz/AutoPatcher/ApGPackages/Java/bin/jar
/cygdrive/d/Janusz/AutoPatcher/ApGPackages/Java/bin/java
/cygdrive/d/Janusz/AutoPatcher/ApGPackages/cygwin/bin/cpio

### verify ROM ###
### running ./auto_patcher /cygdrive/d/Janusz/AutoPatcher/FXP210_cm-10-20130309-UNOFFICIAL-haida_x01.zip openpdroid cm
PATH= /cygdrive/d/Janusz/AutoPatcher/ApGPackages/ap/tmp20130312070942:/cygdrive/d/Janusz/AutoPatcher/ApGPackages/Java/bin:/cygdrive/d/Janusz/AutoPatcher/ApGPackages/cygwin/bin:/cygdrive/d/Janusz/AutoPatcher/ApGPackages/cygwin/usr/sbin

### unzip patch tools ###

### unzip patch patches ###

... result of ROM check: RIL= SemcRIL

### probe rom type ###
#### Standard Build Query ####
# VER= v2.8.51
# OS= cygwin 32bit
# VID= 4.1.2
# PID= openpdroid
# MID= cm_haida-userdebug
# RID= cm
# ANDR= 4.1
# BDID= 20130309
# DID= haida
# BID= 20130209
Patches are openpdroid/4.1/cm/20130209
### DELETE FILES=
### COPY FILES= system/media/PDroid.jpeg
### JAR FILES= system/framework/framework.jar system/framework/core.jar system/framework/services.jar
### APK FILES= system/app/Mms.apk
### IMG FILES=
### TXT FILES=

### unzip rom ###

### create updater script ###

... using Clockworkmod installer ...
# generated updater-script
ui_print("");
ui_print("");
ui_print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~");
ui_print("* *");
ui_print("* * The Auto-Patcher * *");
ui_print("* * * * * *");
ui_print("* * by mateor * *");
ui_print("* *");
ui_print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~");
ui_print("");
ui_print(" Attention");
ui_print(" ************************************");
ui_print("");
ui_print(" There is nothing that can go wrong here");
ui_print(" that reflashing your ROM won't fix.");
ui_print("");
mount("yaffs2", "MTD", "system", "/system");
package_extract_dir("system", "/system");
set_perm_recursive(0, 0, 0755, 0644, "/system");
set_perm_recursive(0, 0, 0755, 0755, "/system/addon.d");
set_perm_recursive(0, 2000, 0755, 0755, "/system/bin");
set_perm(0, 3003, 02750, "/system/bin/netcfg");
set_perm(0, 3004, 02755, "/system/bin/ping");
set_perm(0, 2000, 06750, "/system/bin/run-as");
set_perm_recursive(1002, 1002, 0755, 0440, "/system/etc/bluetooth");
set_perm(0, 0, 0755, "/system/etc/bluetooth");
set_perm(1000, 1000, 0640, "/system/etc/bluetooth/auto_pairing.conf");
set_perm(3002, 3002, 0444, "/system/etc/bluetooth/blacklist.conf");
set_perm(1002, 1002, 0440, "/system/etc/dbus.conf");
set_perm(1014, 2000, 0550, "/system/etc/dhcpcd/dhcpcd-run-hooks");
set_perm_recursive(0, 2000, 0755, 0755, "/system/etc/init.d");
set_perm(0, 0, 0755, "/system/etc/init.d");
set_perm(0, 2000, 0550, "/system/etc/init.goldfish.sh");
set_perm_recursive(0, 0, 0755, 0555, "/system/etc/ppp");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor");
set_perm(0, 0, 0644, "/system/vendor/etc/audio_effects.conf");
set_perm_recursive(0, 2000, 0755, 0755, "/system/xbin");
set_perm(0, 0, 06755, "/system/xbin/librank");
set_perm(0, 0, 06755, "/system/xbin/procmem");
set_perm(0, 0, 06755, "/system/xbin/procrank");
set_perm(0, 0, 06755, "/system/xbin/su");
unmount("/system");
ui_print(" .");
ui_print(" .");
ui_print(" done!");

### create restore.zip ###

### decompile system files ###

... decompile framework.jar ...

... extract preloaded-classes ...
inflated: preloaded-classes

... decompile core.jar ...

... decompile services.jar ...
inflated: system/framework/framework-res.apk

... installing framework files ...

... decompile Mms.apk ...
### copy patch openpdroid/4.1/cm/20130209 ###

... copying system/media/PDroid.jpeg ...
`patches/openpdroid/4.1/cm/20130209/system/media/PDroid.jpeg' -> `./system/media/PDroid.jpeg'

... overwriting GsmServiceStateTracker.smali ...
### delete patch openpdroid/4.1/cm/20130209 ###
### jar patch openpdroid/4.1/cm/20130209 ###

... apply framework.patch ...
The next patch would create the file 'smali/android/app/ContextImpl$40.smali',
which already exists! Skipping patch.
1 out of 1 hunk ignored
5 out of 5 hunks FAILED -- saving rejects to file smali/android/content/ContentResolver.smali.rej
Reversed (or previously applied) patch detected! Skipping patch.
6 out of 6 hunks ignored -- saving rejects to file smali/android/view/ViewGroup.smali.rej
1 out of 5 hunks FAILED -- saving rejects to file smali/com/android/internal/telephony/gsm/GsmServiceStateTracker.smali.rej

... apply preloaded.patch ...

!!! PATCHING FAILED FOR android/content/ContentResolver.smali com/android/internal/telephony/gsm/GsmServiceStateTracker.smali !!!
!!! patch error for android/content/ContentResolver.smali !!!

File for which patching failed:

---------------------------------------------

ContentResolver.smali

You only need to report this if running the program gives you problems!!!
askconsent final = yes: for android/content/ContentResolver.smali

... replace android/content/ContentResolver.smali ...
`patches/openpdroid/4.1/.provisionals/system/framework/framework.jar.out/smali/android/content/ContentResolver.smali' -> `tmp/system/framework/framework.jar.out/smali/android/content/ContentResolver.smali'
!!! patch error for com/android/internal/telephony/gsm/GsmServiceStateTracker.smali !!!

File for which patching failed:

---------------------------------------------

GsmServiceStateTracker.smali

You only need to report this if running the program gives you problems!!!
askconsent final = yes: for com/android/internal/telephony/gsm/GsmServiceStateTracker.smali

... replace com/android/internal/telephony/gsm/GsmServiceStateTracker.smali ...
`patches/openpdroid/4.1/.provisionals/system/framework/framework.jar.out/smali/com/android/internal/telephony/gsm/GsmServiceStateTracker.smali' -> `tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/gsm/GsmServiceStateTracker.smali'
GARBAGE= tmp/system/framework/framework.jar.out/smali/android/app/ContextImpl.smali.orig
GARBAGE= tmp/system/framework/framework.jar.out/smali/android/view/ViewGroup.smali.rej

... apply core.patch ...
GARBAGE=
GARBAGE=

... apply services.patch ...
GARBAGE=
GARBAGE=
### apk patch openpdroid/4.1/cm/20130209 ###

... apply Mms.apk.patch ...
21 out of 21 hunks FAILED -- saving rejects to file smali/com/android/mms/transaction/HttpUtils.smali.rej
`patches/openpdroid/4.1/cm/20130209/system/app/Mms.apk' -> `system/app/Mms.apk'
GARBAGE= tmp/system/app/Mms.apk.out/smali/com/android/mms/transaction/HttpUtils.smali.orig
GARBAGE= tmp/system/app/Mms.apk.out/smali/com/android/mms/transaction/HttpUtils.smali.rej
### img patch openpdroid/4.1/cm/20130209 ###
### text patch openpdroid/4.1/cm/20130209 ###

### rebuild jar ###

... rebuild framework.jar ...

UNEXPECTED TOP-LEVEL EXCEPTION:
org.jf.dexlib.Util.ExceptionWithContext: method index is too large.
at org.jf.dexlib.Util.ExceptionWithContext.withContext(ExceptionWithContext.java:54)
at org.jf.dexlib.Item.addExceptionContext(Item.java:177)
at org.jf.dexlib.Item.writeTo(Item.java:120)
at org.jf.dexlib.Section.writeTo(Section.java:119)
at org.jf.dexlib.DexFile.writeTo(DexFile.java:716)
at org.jf.smali.main.main(main.java:227)
Caused by: java.lang.RuntimeException: method index is too large.
at org.jf.dexlib.Code.Format.Instruction35c.writeInstruction(Instruction35c.java:102)
at org.jf.dexlib.Code.Instruction.write(Instruction.java:57)
at org.jf.dexlib.CodeItem.writeItem(CodeItem.java:258)
at org.jf.dexlib.Item.writeTo(Item.java:117)
... 3 more
code_item @0x193f00 (Landroid/accessibilityservice/AccessibilityServiceInfo;-><init>(Landroid/content/pm/ResolveInfo;Landroid/content/Context;)V)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!!! error: failed compiling framework.jar !!!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!!! Problem with method cap !!!

... attempting fix ...

... remove unnecessary 27 files to avoid methods cap ...
DELETE RILS= tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/HTCQualcommRIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/LGEQualcommRIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/LGEQualcommUiccRIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/MotoWrigley3GRIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/QualcommSharedRIL$1.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/QualcommSharedRIL$IccHandler.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/QualcommSharedRIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungCDMAQualcommRIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungCDMAv6RIL$1.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungCDMAv6RIL$ConnectivityHandler$ConnectivityBroadcastReceiver.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungCDMAv6RIL$ConnectivityHandler.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungCDMAv6RIL$SamsungDriverCall.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungCDMAv6RIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungHCRIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungQualcommD2RIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungQualcommUiccRIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungRIL$1.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungRIL$ConnectivityHandler$ConnectivityBroadcastReceiver.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungRIL$ConnectivityHandler.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungRIL$SamsungDriverCall.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SamsungRIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/Smdk4210RIL$1.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/Smdk4210RIL$ConnectivityHandler$ConnectivityBroadcastReceiver.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/Smdk4210RIL$ConnectivityHandler.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/Smdk4210RIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SonyQualcommRIL.smali tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/SonyQualcommRIL7x27a.smali

... rebuild framework.jar ...
adding: classes.dex(in = 8797660) (out= 3545088)(deflated 59%)
adding: preloaded-classes(in = 84887) (out= 14594)(deflated 82%)

... rebuild core.jar ...
adding: classes.dex(in = 2512068) (out= 1045773)(deflated 58%)

... rebuild services.jar ...
adding: classes.dex(in = 1818220) (out= 815793)(deflated 55%)

### rebuild apk ###

... rebuild Mms.apk ...
I: Checking whether sources has changed...
I: Smaling...
I: Checking whether resources has changed...
I: Building resources...
I: Building apk file...

### create update-cm-haida-20130309-openpdroid.zip ###
added manifest
adding: system/framework/framework.jar(in = 3560233) (out= 3535797)(deflated 0%)
adding: system/framework/core.jar(in = 1050011) (out= 1043836)(deflated 0%)
adding: system/framework/services.jar(in = 816252) (out= 814984)(deflated 0%)
adding: system/app/Mms.apk(in = 3987173) (out= 3736964)(deflated 6%)
adding: system/media/PDroid.jpeg(in = 26898) (out= 25744)(deflated 4%)
ignoring entry META-INF/
adding: META-INF/com/(in = 0) (out= 0)(stored 0%)
adding: META-INF/com/google/(in = 0) (out= 0)(stored 0%)
adding: META-INF/com/google/android/(in = 0) (out= 0)(stored 0%)
adding: META-INF/com/google/android/update-binary(in = 193136) (out= 124459)(deflated 35%)
adding: META-INF/com/google/android/updater-script(in = 2266) (out= 515)(deflated 77%)