I was ripping a CD, surfing the web and uploading via USB and 2.03Beta and I kept getting warning during the "uploading tunes" step... "timed out on tune xxx".

When the sync was done, 1/2 of the tunes from each album was not uploaded. I ended all other tasks on the computer and re-sync'd, and all went fine.

I am not sure if the multi-tasking was related, but it is the only thing I could come up with.