[Motorola Droid and Milestone Q&A, Help & Troublesh] Tal_Star:
I've pasted a copy of the log bellow.

ROOT= /cygdrive/c/Temp/ApGPackages/ap/
TOOL= /cygdrive/c/Temp/ApGPackages/ap//patch_tools.tgz
ROM= /cygdrive/c/Temp/cm-7.2.3-umts_sholes.zip
ROMX= C:\Temp\CM-723~1.ZIP

### verify tools ###
/cygdrive/c/Temp/ApGPackages/cygwin/bin/patch
/cygdrive/c/Temp/ApGPackages/cygwin/bin/tar
/cygdrive/c/Temp/ApGPackages/Java/bin/jar
/cygdrive/c/Temp/ApGPackages/Java/bin/java
/cygdrive/c/Temp/ApGPackages/cygwin/bin/cpio

### verify ROM ###
### running ./auto_patcher /cygdrive/c/Temp/cm-7.2.3-umts_sholes.zip pdroid cm7
PATH= /cygdrive/c/Temp/ApGPackages/ap/tmp20121022100213:/cygdrive/c/Temp/ApGPackages/Java/bin:/cygdrive/c/Temp/ApGPackages/cygwin/bin:/cygdrive/c/Temp/ApGPackages/cygwin/usr/sbin

### unzip patch tools ###

### unzip patch patches ###

... result of ROM check: RIL= motow3g

### probe rom type ###
# VER= Auto-Patcher v2.1.9
# OS= cygwin 32bit
# VID= 2.3.7
# MID=
# RID= cm7
# BDID= 2011-01-18
# DID=
# BID= latest
# PID= pdroid
### DELETE FILES=
### COPY FILES=
### JAR FILES= system/framework/framework.jar system/framework/core.jar system/framework/services.jar
### APK FILES=
### IMG FILES=
### TXT FILES=

### unzip rom ###

### create updater script ###

... using Clockworkmod installer ...
# generated updater-script
mount("yaffs2", "MTD", "system", "/system");
package_extract_dir("system", "/system");
set_perm_recursive(0, 0, 0755, 0644, "/system");
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, 1000, 04755, "/system/bin/pppd");
set_perm(0, 2000, 06750, "/system/bin/run-as");
set_perm(1000, 1003, 02755, "/system/bin/screenshot");
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, 0750, "/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, 0755, "/system/xbin");
set_perm(0, 0, 06755, "/system/xbin/hcitool");
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");
set_perm(0, 0, 06755, "/system/xbin/tcpdump");
unmount("/system");

### create restore.zip ###

### decompile system files ###

... decompile framework.jar ...

UNEXPECTED TOP-LEVEL EXCEPTION:
org.jf.dexlib.DexFile$NoClassesDexException: zip file framework.jar does not contain a classes.dex file
at org.jf.dexlib.DexFile.<init>(DexFile.java:298)
at org.jf.baksmali.main.main(main.java:269)

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

... decompile core.jar ...

UNEXPECTED TOP-LEVEL EXCEPTION:
org.jf.dexlib.DexFile$NoClassesDexException: zip file core.jar does not contain a classes.dex file
at org.jf.dexlib.DexFile.<init>(DexFile.java:298)
at org.jf.baksmali.main.main(main.java:269)

... decompile services.jar ...

UNEXPECTED TOP-LEVEL EXCEPTION:
org.jf.dexlib.DexFile$NoClassesDexException: zip file services.jar does not contain a classes.dex file
at org.jf.dexlib.DexFile.<init>(DexFile.java:298)
at org.jf.baksmali.main.main(main.java:269)

### jar patch pdroid/cm7/latest ###

... apply framework.patch ...

... apply preloaded.patch ...

... apply core.patch ...

... apply services.patch ...

### rebuild jar ###

... rebuild framework.jar ...

UNEXPECTED TOP-LEVEL EXCEPTION:
java.lang.RuntimeException: Cannot find file or directory "tmp/system/framework/framework.jar.out/smali"
at org.jf.smali.main.main(main.java:184)