IPhone not syncing properly with iTunes 10.5

Hi,
I recently updated my iPhone 4 to the iOS 5 and also updated my iTunes to 10.5. A few days later I got an error message on my iTunes which said that the library was damaged, it would create and new one and save the 'old' one has "iTunes Library (Damaged)". Shortly after I synced my phone with iTunes and it removed many of my apps and all my playlists and music. I've re-downloaded all my apps, though any pictures, settings, etc saved within them have disappeared. I cleared the music on my phone and re-synced it. Any playlists which were re-synced only actually synced recently added songs (i.e. if a playlist had 20 songs and I added 3 more only those 3 would show up on my phone).
I think all my data, apps, etc are still on the phone but iTunes isn't recognising it; any ideas of how to get iTunes to recognise it?
Thanks!
If it helps or makes a difference, I'm using Windows Vista.

Same thing (?) is happening with my iPhone4. Syncing wirelessly doesn't work at all, and when I connect it to my Mac, sync gets stuck on 'Syncing Genius Data to _____' and under that it says "waiting for items to copy". This is also the case with my iPod Touch 4th gen. Both are on iOS5 and I have the latest iTunes. So I just backup both of them, and then choose the sync button on bottom right of iTunes in the device window. Don't know if it's actually doing anything.
This *****.

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