I had this exact problem, just as described by the original poster. I went to the Apple store, but the Genius Bar was totally unable to help. I am glad I went, however, in that they did have a possible explanation, which was as alarming as it was unexpected: the backup files are probably corrupt (in my case, perhaps by an (unwanted) simultaneous iOS upgrade to 4.02?). Apple had no solution, but the only choice I can see is restoring a previous, good version of the backup image to your computer, and then trying the restore again. Hopefully you have Time Machine or something similar--for once in my life, I am prepared. The files in question are located in different places on Mac and PC. See:
http://forums.macnn.com/103/ipod-iphone-and-ipad/355013/iphone-backup-file-locat ion/)
Restore the entire folder, just to be safe. iTunes now accepts the backup and seems to be working normally. It has reset, and the full restore is in process. I won't know for a few hours if my all app data is intact, so I'll have to report back.
PS: Do to some panicky monkeying around earlier in the day, I also had to restore earlier versions of these 3 files to make it work, as iTunes was no longer recognizing the old image files as belonging to my iPod. I'm not sure which one is truly responsible for the confusion.
1) iTunes Library.itl
2) iTunes Library Extras.itdb
3) sentinel