Similar problem...
Ever since i updated the itunes to 9.0, my iPhone 3GS just stopped backing up. Before, the backup was fairly quick, and now, sometimes it doesn't even get pass the diagonal lines, and if it does, the backup is REAL slow.
I've looked around on other forums and there were some suggestions on deleting the iTunes preference files, which I did, and by doing that it still didn't resolve my issue. I have also looked at my backed-up files, but none of them could be corrupted because they were the ones that were "backed up" after this whole problem occured, which is another thing I don't understand. I always X out of the backup thing when it gets to the diagonal lines after I wait for a long time, but then it shows up in my backup list of previous backups. Does it mean that iTunes actually backed my phone up?
Anyway, if anyone could please let me know how I can get my phone to back up properly again as I want to upgrade to iOS4 with no problems! Thanks