I'm confused. You said it does save it, but it's not backed up? I just updating to 5.1.1 and do not plan on jailbreaking again until after iOS 6 so for the mean time I do not care about my themes. My only question is, if I restore my phone from my jailbroken backup, are the themes in that back up (even though I would be using them)? I ask because I just did it to try it, and my "other" category decreased by 1.2 GB, so I was not sure if that means it's gone, or it's still there but itunes doesn't recognize it as taking up space.Correct iTunes does save jb tweaks themes etc. Most of it in iTunes is displayed as other but is not backed up. There is pkgbackup and xbackup in Cydia that were designed to back those up.