[Android Software/Hacking General [Developers Only]] xpria2012:
I'd like to report that I was able to patch the ROM with the Auto-Patcher v2.6.0, however, in a really strange way. If you could take a look at the log:

$ ./auto_patcher FXP204-cm-9-20130126-UNOFFICIAL-nypon.zip pdroid,v6supercharger

The Auto-Patcher v2.6.0

### verify tools ###
### verify ROM ###
### unzip patch tools ###
### unzip patch patches ###
inflated: system/build.prop
### 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 ...
The next patch would create the file 'smali/android/app/ContextImpl$36.smali',
which already exists! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file 'smali/android/app/ContextImpl$36.smali.rej'
Reversed (or previously applied) patch detected! Skipping patch.
38 out of 38 hunks ignored -- saving rejects to file smali/android/net/wifi/WifiConfigStore.smali.rej
Reversed (or previously applied) patch detected! Skipping patch.
15 out of 15 hunks ignored -- saving rejects to file 'smali/com/android/internal/telephony/RIL$RILSender.smali.rej'
Reversed (or previously applied) patch detected! Skipping patch.
4 out of 4 hunks ignored -- saving rejects to file 'smali/com/android/internal/telephony/sip/SipPhone$SipConnection.smali.rej'
... apply preloaded.patch ...
... apply core.patch ...
... apply services.patch ...
./auto_patcher: line 1343: patches/pdroid/4.0/cm/20120811/services.patch: No such file or directory
cat: services.jar.log: No such file or directory
grep: services.jar.log: No such file or directory
grep: services.jar.log: No such file or directory
### jar patch v6supercharger/4.0/cm/latest ###
... apply services.patch ...
### rebuild jar ###
... rebuild framework.jar ...
... rebuild core.jar ...
... rebuild services.jar ...
### create update-cm-nypon-20130126-pdroid-v6supercharger.zip ###
### finished ###
flash update-cm-nypon-20130126-pdroid-v6supercharger.zip to install the patched files
flash restore-cm-nypon-20130126.zip to restore the original system

So the log prints this line "./auto_patcher: line 1343: patches/pdroid/4.0/cm/20120811/services.patch: No such file or directory", and when I unpack patch_patches.tgz, (for \patches\pdroid\4.0\cm), I only see the 20120811 folder (no earlier patches). And in that folder there are core.patch, preloaded.patch and services.patch files with 0 byte sizes, also a framework.patch with the size of 742.276 bytes and a framework.patch~ with the size of 742.303 bytes. Packed sizes of all files appear "?". I originally thought that the files are downloaded wrong, but two other attempts to download generated the same results (if these aren't the right file characteristics, maybe the upload is broken?). I also checked the files in the update.zip, and all 3 files have different file sizes from the original files in the ROM, so the patcher generated different files. I didn't try the patch on my phone yet because I couldn't figure out if this patch is broken or not.

About the ROM not patching, sure, I have tried to patch plenty of ROM's (also for other devices) in the past and I get that some (especially the stock based ones) just won't patch (sadly, there is no ROM other than CM and stock-based ROM's for my device, and the only ones that patch are the obsolete ones now). What I don't get is, according to FreeXperia Team's changelog, their update the ROM from FXP202 (the latest version that patched successfully) to FXP203 (the first version that didn't patch successfully) was adding a governor, which isn't even related to the success of this patch, except compiling the latest CM9.1 sources into the ROM. Moreover, dangerzone and samsara00 also reported in this thread that they can't patch FreeXperia's ROM's (for a different device) above the version FXP202, so if this patch I did was broken too, it seems like there is something wrong with the CM sources of FreeXperia Team, and I will contact them about this issue.

Lastly, this project is like the proof that the best things in life are free. I just don't know how to thank you guys for developing, and also providing support for, something this awesome expecting no monetary gain whatsoever. It's almost not fair :D. Anyway my biggest thanks to you all who make this project exist today!