I had a similar problem. Had a failed 3.0 upgrade (1604 error). I removed and installed itunes 8.x. Then I reinstalled 8.2. Still had 1604. (did not know what 1604 meant at the time.) I did upgrade on a different PC but of course I had no music, apps, data, or settings. When I went back to synch on original PC, iphone would not synch music. Also, recent songs purchased through itunes would not play in itunes. Older itunes purchased did play in itunes. I called apple and was on the phone for 45 minutes, they did a one time re-enablement of all my music. Still did not work. They sent me an email a few days a later saying to remove quick time, then remove itunes. Then I was to reboot and reinstall quicktime from their website. Then I was to install itunes 8.2 again. Now all the music started playing in itunes. However it still would not synch to phone. I had to remove all music from the phone and then the resynch worked and music played.
This all was on my daughters non-jailbroken 3g 16gb iphone.
Try calling apple, they may be able to help.