[Android Software/Hacking General [Developers Only]] mithrial:
Thank you for your fast answers.

I hope I understood you correctly.

I redownloaded the newest nightly (cm-7-20120624-NIGHTLY-bravo) and patched it with ./auto_patcher cm-7-20120624-NIGHTLY-bravo.zip pdroid cm7 20120514.

The output of the script was the same like before (it used 20120514 instead of latest of course).

The log is mainly the same but there are some differences, maybe they are important.

### verify tools ###
/usr/bin/patch
/bin/tar
/usr/bin/jar
/usr/local/java/jdk1.7.0_05/bin/java
### verify ROM ###
# running ./auto_patcher cm-7-20120624-NIGHTLY-bravo.zip pdroid cm7 20120514
### unzip patch tools ###
baksmali.jar
signapk.jar
smali.jar
updatecert.pem
updatekey.pk8
update-template.zip
### unzip patch patches ###
patches/
patches/v6supercharger/
patches/v6supercharger/files.txt
patches/v6supercharger/generic
patches/v6supercharger/cm9/
patches/v6supercharger/cm9/latest
patches/v6supercharger/cm9/20120614/
patches/v6supercharger/cm9/20120614/services.patch
patches/pdroid/
patches/pdroid/common/
patches/pdroid/common/20120506/
patches/pdroid/common/20120506/preloaded.patch
patches/pdroid/common/20120506/core.patch
patches/pdroid/common/latest
patches/pdroid/files.txt
patches/pdroid/generic
patches/pdroid/cm9/
patches/pdroid/cm9/20120601/
patches/pdroid/cm9/20120601/services.patch
patches/pdroid/cm9/20120601/preloaded.patch
patches/pdroid/cm9/20120601/framework.patch
patches/pdroid/cm9/20120601/core.patch
patches/pdroid/cm9/20120506/
patches/pdroid/cm9/20120506/services.patch
patches/pdroid/cm9/20120506/preloaded.patch
patches/pdroid/cm9/20120506/framework.patch
patches/pdroid/cm9/20120506/core.patch
patches/pdroid/cm9/latest
patches/pdroid/cm9/20120615/
patches/pdroid/cm9/20120615/services.patch
patches/pdroid/cm9/20120615/preloaded.patch
patches/pdroid/cm9/20120615/framework.patch
patches/pdroid/cm9/20120615/core.patch
patches/pdroid/cm9/20120508/
patches/pdroid/cm9/20120508/services.patch
patches/pdroid/cm9/20120508/preloaded.patch
patches/pdroid/cm9/20120508/framework.patch
patches/pdroid/cm9/20120508/core.patch
patches/pdroid/aosp/
patches/pdroid/aosp/20120506/
patches/pdroid/aosp/20120506/services.patch
patches/pdroid/aosp/20120506/preloaded.patch
patches/pdroid/aosp/20120506/framework.patch
patches/pdroid/aosp/20120506/core.patch
patches/pdroid/aosp/20120507/
patches/pdroid/aosp/20120507/services.patch
patches/pdroid/aosp/20120507/preloaded.patch
patches/pdroid/aosp/20120507/framework.patch
patches/pdroid/aosp/20120507/core.patch
patches/pdroid/aosp/latest
patches/pdroid/aosp/20120515/
patches/pdroid/aosp/20120515/services.patch
patches/pdroid/aosp/20120515/preloaded.patch
patches/pdroid/aosp/20120515/framework.patch
patches/pdroid/aosp/20120515/core.patch
patches/pdroid/aokp/
patches/pdroid/aokp/20120613/
patches/pdroid/aokp/20120613/services.patch
patches/pdroid/aokp/20120613/preloaded.patch
patches/pdroid/aokp/20120613/framework.patch
patches/pdroid/aokp/20120613/core.patch
patches/pdroid/aokp/20120506/
patches/pdroid/aokp/20120506/services.patch
patches/pdroid/aokp/20120506/preloaded.patch
patches/pdroid/aokp/20120506/framework.patch
patches/pdroid/aokp/20120506/core.patch
patches/pdroid/aokp/latest
patches/pdroid/aokp/20120510/
patches/pdroid/aokp/20120510/services.patch
patches/pdroid/aokp/20120510/preloaded.patch
patches/pdroid/aokp/20120510/framework.patch
patches/pdroid/aokp/20120510/core.patch
patches/pdroid/cm7/
patches/pdroid/cm7/20120619/
patches/pdroid/cm7/20120619/services.patch
patches/pdroid/cm7/20120619/preloaded.patch
patches/pdroid/cm7/20120619/framework.patch
patches/pdroid/cm7/20120619/core.patch
patches/pdroid/cm7/latest
patches/pdroid/cm7/20120514/
patches/pdroid/cm7/20120514/services.patch
patches/pdroid/cm7/20120514/preloaded.patch
patches/pdroid/cm7/20120514/framework.patch
patches/pdroid/cm7/20120514/core.patch
patches/pdroid/cm7/patch_patches.tgz
# VID=
# MID=
# RID= cm7
# DID=
# BID= 20120514
# PID= pdroid
### FILES= system/framework/framework.jar system/framework/core.jar system/framework/services.jar
### unzip rom ###
### create updater script ###
### using Clockworkmod installer ###
# generated updater-script
mount("yaffs2", "MTD", "system", "/system");
package_extract_dir("system", "/system");
unmount("/system");
### create restore.zip ###
added manifest
adding: system/framework/framework.jar(in = 3111222) (out= 3093059)(deflated 0%)
adding: system/framework/core.jar(in = 1862816) (out= 1851861)(deflated 0%)
adding: system/framework/services.jar(in = 684722) (out= 683710)(deflated 0%)
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 = 194664) (out= 125211)(deflated 35%)
adding: META-INF/com/google/android/updater-script(in = 107) (out= 66)(deflated 38%)
### decompile framework.jar ###
... extract preloaded-classes ...
inflated: preloaded-classes
### decompile core.jar ###
### decompile services.jar ###
### apply framework.patch ###
GARBAGE= tmp/system/framework/framework.jar.out/smali/com/google/android/mms/pdu/PduPersister.smali.orig
GARBAGE=
... apply preloaded.patch ...
### apply core.patch ###
GARBAGE=
GARBAGE=
### apply services.patch ###
GARBAGE=
GARBAGE=
### rebuild framework.jar ###
adding: classes.dex(in = 6369612) (out= 2625827)(deflated 58%)
adding: preloaded-classes(in = 65633) (out= 11974)(deflated 81%)
### rebuild core.jar ###
adding: classes.dex(in = 3586768) (out= 1501170)(deflated 58%)
### rebuild services.jar ###
adding: classes.dex(in = 1278532) (out= 580006)(deflated 54%)
### create updater.zip ###
added manifest
adding: system/framework/framework.jar(in = 2638386) (out= 2619732)(deflated 0%)
adding: system/framework/core.jar(in = 1524210) (out= 1514183)(deflated 0%)
adding: system/framework/services.jar(in = 580465) (out= 579824)(deflated 0%)
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 = 194664) (out= 125211)(deflated 35%)
adding: META-INF/com/google/android/updater-script(in = 107) (out= 66)(deflated 38%)

The error stays the same.

I attached the full log but here are some excerpts:

D/dalvikvm( 136): DexOpt: --- BEGIN 'core.jar' (bootstrap=1) ---
D/dalvikvm( 190): creating instr width table
E/dalvikvm( 190): ERROR: Can't byte swap: bad dex version (0x30 33 36 00)
E/dalvikvm( 190): ERROR: Byte swap + verify failed
E/dalvikvm( 190): Optimization failed
W/dalvikvm( 136): DexOpt: --- END 'core.jar' --- status=0xff00, process failed
E/dalvikvm( 136): Unable to extract+optimize DEX from '/system/framework/core.jar'
D/dalvikvm( 136): Unable to process classpath element '/system/framework/core.jar'
D/dalvikvm( 136): DexOpt: incorrect opt magic number (0xff ff ff ff)
D/dalvikvm( 136): ODEX file is stale or bad; removing and retrying (/data/dalvik-cache/system@framework@bouncycastle.jar@classes.dex)
D/dalvikvm( 136): DexOpt: --- BEGIN 'bouncycastle.jar' (bootstrap=1) ---
D/dalvikvm( 192): creating instr width table
E/dalvikvm( 192): Too many exceptions during init (failed on 'Ljava/lang/NoClassDefFoundError;' 'java.lang.NoClassDefFoundError')
E/dalvikvm( 192): VM aborting

W/dalvikvm( 136): DexOpt: --- END 'bouncycastle.jar' --- status=0x000b, process failed
E/dalvikvm( 136): Unable to extract+optimize DEX from '/system/framework/bouncycastle.jar'
D/dalvikvm( 136): Unable to process classpath element '/system/framework/bouncycastle.jar'
D/dalvikvm( 136): DexOpt: incorrect opt magic number (0xff ff ff ff)
D/dalvikvm( 136): ODEX file is stale or bad; removing and retrying (/data/dalvik-cache/system@framework@ext.jar@classes.dex)
D/dalvikvm( 136): DexOpt: --- BEGIN 'ext.jar' (bootstrap=1) ---
D/dalvikvm( 193): creating instr width table
E/dalvikvm( 193): Too many exceptions during init (failed on 'Ljava/lang/NoClassDefFoundError;' 'java.lang.NoClassDefFoundError')
E/dalvikvm( 193): VM aborting
I/DEBUG ( 134): *** *** *** *** *** *** *** *** *** *** *** *** *** *** *** ***

W/dalvikvm( 136): DexOpt: --- END 'ext.jar' --- status=0x000b, process failed
E/dalvikvm( 136): Unable to extract+optimize DEX from '/system/framework/ext.jar'
D/dalvikvm( 136): Unable to process classpath element '/system/framework/ext.jar'
D/dalvikvm( 136): DexOpt: incorrect opt magic number (0xff ff ff ff)
D/dalvikvm( 136): ODEX file is stale or bad; removing and retrying (/data/dalvik-cache/system@framework@framework.jar@classes.dex)
D/dalvikvm( 136): DexOpt: --- BEGIN 'framework.jar' (bootstrap=1) ---
D/dalvikvm( 196): creating instr width table
E/dalvikvm( 196): ERROR: Can't byte swap: bad dex version (0x30 33 36 00)
E/dalvikvm( 196): ERROR: Byte swap + verify failed
E/dalvikvm( 196): Optimization failed
W/dalvikvm( 136): DexOpt: --- END 'framework.jar' --- status=0xff00, process failed
E/dalvikvm( 136): Unable to extract+optimize DEX from '/system/framework/framework.jar'
D/dalvikvm( 136): Unable to process classpath element '/system/framework/framework.jar'
D/dalvikvm( 136): DexOpt: incorrect opt magic number (0xff ff ff ff)
D/dalvikvm( 136): ODEX file is stale or bad; removing and retrying (/data/dalvik-cache/system@framework@android.policy.jar@classes.dex)
D/dalvikvm( 136): DexOpt: --- BEGIN 'android.policy.jar' (bootstrap=1) ---
D/dalvikvm( 197): creating instr width table
E/dalvikvm( 197): Too many exceptions during init (failed on 'Ljava/lang/NoClassDefFoundError;' 'java.lang.NoClassDefFoundError')
E/dalvikvm( 197): VM aborting

W/dalvikvm( 136): DexOpt: --- END 'android.policy.jar' --- status=0x000b, process failed
E/dalvikvm( 136): Unable to extract+optimize DEX from '/system/framework/android.policy.jar'
D/dalvikvm( 136): Unable to process classpath element '/system/framework/android.policy.jar'
D/dalvikvm( 136): DexOpt: incorrect opt magic number (0xff ff ff ff)
D/dalvikvm( 136): ODEX file is stale or bad; removing and retrying (/data/dalvik-cache/system@framework@services.jar@classes.dex)
D/dalvikvm( 136): DexOpt: --- BEGIN 'services.jar' (bootstrap=1) ---
D/dalvikvm( 198): creating instr width table
E/dalvikvm( 198): ERROR: Can't byte swap: bad dex version (0x30 33 36 00)
E/dalvikvm( 198): ERROR: Byte swap + verify failed
E/dalvikvm( 198): Optimization failed
W/dalvikvm( 136): DexOpt: --- END 'services.jar' --- status=0xff00, process failed
E/dalvikvm( 136): Unable to extract+optimize DEX from '/system/framework/services.jar'
D/dalvikvm( 136): Unable to process classpath element '/system/framework/services.jar'
D/dalvikvm( 136): DexOpt: incorrect opt magic number (0xff ff ff ff)
D/dalvikvm( 136): ODEX file is stale or bad; removing and retrying (/data/dalvik-cache/system@framework@core-junit.jar@classes.dex)
D/dalvikvm( 136): DexOpt: --- BEGIN 'core-junit.jar' (bootstrap=1) ---
D/dalvikvm( 199): creating instr width table
E/dalvikvm( 199): Too many exceptions during init (failed on 'Ljava/lang/NoClassDefFoundError;' 'java.lang.NoClassDefFoundError')
E/dalvikvm( 199): VM aborting

W/dalvikvm( 136): DexOpt: --- END 'core-junit.jar' --- status=0x000b, process failed
E/dalvikvm( 136): Unable to extract+optimize DEX from '/system/framework/core-junit.jar'
D/dalvikvm( 136): Unable to process classpath element '/system/framework/core-junit.jar'
E/dalvikvm( 136): No valid entries found in bootclasspath '/system/framework/core.jar:/system/framework/bouncycastle.jar:/system/framework/ext.jar:/system/framework/framework.jar:/system/framework/android.policy.jar:/system/framework/services.jar:/system/framework/core-junit.jar'
W/dalvikvm( 136): JNI_CreateJavaVM failed
E/AndroidRuntime( 136): JNI_CreateJavaVM failed
I/ServiceManager( 131): service 'media.audio_flinger' died
I/ServiceManager( 131): service 'media.player' died
I/ServiceManager( 131): service 'media.camera' died
I/ServiceManager( 131): service 'media.audio_policy' died

Then in starts from the beginning