Can't sync iphone with Mac after restoring from TimeMachine I recently reinstalled my MacBook from a time machine backup (because I installed an SSD) [*]. Now syncing my iPhone via iTunes doesn't seem to work anymore:

At first, it displayed "over capacity" by 3.4 GB (which makes no sense, as I haven't added anything)

Then, after deleting several apps from my iPhone, the "over capacity" message is gone, but syncing doesn't work:


At first, it appears to work normally, and the capacity bar starts to fill up green on the left (green = apps)
Then, after it finishes, the capacity bar turns yellow: 
I'm trying to sync a few files (just one song, and a few books), but they all keep the sync icon and are grayed out  I can't access the files on my iPhone.


Also, my iPhone seems to believe that the last backup to my computer was in September (according to Settings > General > iTunes Wi-Fi Sync), whereas iTunes says, that the last backup was today.

How can I make the setup work again? I tried enabling/disabling "Manually manage music and videos" and "Sync only checked songs and videos", as well as "Sync Apps" etc.

Info: Mac OS X 10.6.8, iOS 5.1.1, not using iCloud - only backing up to this mac.

[*] as described in http://support.apple.com/kb/HT1427 -> Restoring data from Time Machine backups -> If you are restoring a backup made by a Mac to the same Mac.
After spending almost the entire day on this problem, I found the solution: I had to thoroughly re-install iTunes, using FineWine's step-by-step guide.

Here are the things I did before that, but which had no effect:
- Tweaking every possible setting in iTunes
- tweaking every possible setting on my iPhone
- reinstalling the latest backup
- reinstalling the backup from last month
- reinstalling the backup from a year ago
- deleting files on my phone manually
- doing several iPhone hard resets
- upgrading to iOS 6 (!)
- and more