[Android Software/Hacking General [Developers Only]] xpria2012:
Sure, I took Sony Xperia acro S' (hikari) patches for test. As a recent release, this is the output trying to patch the nightly CM9.1 build of 20130127 (to note, the ROM I was originally trying to patch was also a nightly build)

$ ./auto_patcher cm-9-20130127-NIGHTLY-hikari.zip pdroid,v6supercharger

The Auto-Patcher v2.5.7

### verify tools ###
### verify ROM ###
### unzip patch tools ###
### unzip patch patches ###
inflated: system/build.prop
... result of ROM check: RIL= SonyQualcommRIL
### probe rom type ###
... result of ROM check: version= 4.0.4 rom= cm ...
... Using results of ROM check ...
... pdroid patch date has been set to: 20120811 ...
### unzip rom ###
inflated: system/framework/core.jar
inflated: system/framework/framework.jar
inflated: system/framework/services.jar
### create updater script ###
inflated: META-INF/com/google/android/update-binary
inflated: META-INF/com/google/android/updater-script
... using Clockworkmod installer ...
### create restore.zip ###
### decompile system files ###
... decompile framework.jar ...
... extract preloaded-classes ...
... decompile core.jar ...
... decompile services.jar ...
### jar patch pdroid/4.0/cm/20120811 ###
... apply framework.patch ...
Reversed (or previously applied) patch detected! Skipping patch.
38 out of 38 hunks ignored -- saving rejects to file smali/android/net/wifi/WifiConfigStore.smali.rej
... apply preloaded.patch ...
... apply core.patch ...
... apply services.patch ...
### jar patch v6supercharger/4.0/cm/latest ###
... apply services.patch ...
### rebuild jar ###
... rebuild framework.jar ...

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

!!! This error is generally due to an unknown bug in the smali binary!
In our experience, it goes away if you run the patcher a second time.
Please run the Auto-Patcher with the same command once again.

If after the third attempt the same thing happens,
please upload your logfile to our support thread!

And this is the output trying to patch the stable build of CM9.1 for the same device

$ ./auto_patcher cm-9.1.0-hikari.zip pdroid,v6supercharger

The Auto-Patcher v2.5.7

### verify tools ###
### verify ROM ###
### unzip patch tools ###
### unzip patch patches ###
inflated: system/build.prop
... result of ROM check: RIL= SonyQualcommRIL
### probe rom type ###
... result of ROM check: version= 4.0.4 rom= cm ...
... Using results of ROM check ...
... pdroid patch date has been set to: 20120811 ...
### unzip rom ###
inflated: system/framework/core.jar
inflated: system/framework/framework.jar
inflated: system/framework/services.jar
### create updater script ###
inflated: META-INF/com/google/android/update-binary
inflated: META-INF/com/google/android/updater-script
... using Clockworkmod installer ...
### create restore.zip ###
### decompile system files ###
... decompile framework.jar ...
... extract preloaded-classes ...
... decompile core.jar ...
... decompile services.jar ...
### jar patch pdroid/4.0/cm/20120811 ###
... apply framework.patch ...
Reversed (or previously applied) patch detected! Skipping patch.
38 out of 38 hunks ignored -- saving rejects to file smali/android/net/wifi/WifiConfigStore.smali.rej
... apply preloaded.patch ...
... apply core.patch ...
... apply services.patch ...
### jar patch v6supercharger/4.0/cm/latest ###
... apply services.patch ...
### rebuild jar ###
... rebuild framework.jar ...

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

!!! This error is generally due to an unknown bug in the smali binary!
In our experience, it goes away if you run the patcher a second time.
Please run the Auto-Patcher with the same command once again.

If after the third attempt the same thing happens,
please upload your logfile to our support thread!

Edit: I also can't patch the FXP's CM9.1 ROM for Xperia P (the ROM I originally wanted to patch) with the previous versions of Auto-Patcher for the builds after FXP202 (actually I only tried with FXP203, didn't try with FXP204 but just guessing).