The keyboard on my iPod malfunctioned, and I couldn't get onto it. I then backed it up and restored it. After it was restored, I tried to put my previous files back on it, but only got my pictures and bookmarks on. It says the "other" category is using 2.5GB of space! I am wondering what possibly is going on? (If it helps, it was jailbroken and now is upgraded to iOS 5.1.1).
Anything from applications (non-iTunes apps), saved games, stored files (using OpenSSH for example). Mainly jailbreak items etc ... make up the (Other) in iTunes. Anything that takes up space and can not be recognized by iTunes, shows up as 'other'.
I think what is happening is it is installing things from all of your jailbroken apps even though your device is not jailbroken any more. I think what ZHENJiNG LiANG is saying is to restore your iPod as a new device and then sync everything (music, apps, photos) etc... manually instead of restoring from your backup. Because your backup obviously has files in it that no longer relate to your non jailbroken phone.