Same problem here. 2x iphone 4s's, 2x gen 1 ipad's, Win7 64.
Every night, dozens and dozens, possibly hundreds. I don't count them. But they happen nearly constantly while syncing too, making it impossible to finish a sync anymore.
I find that if I restart my PC, not just iTunes, this will not happen for the first sync. But nearly all syncs after that experience these message popups, it gets worse the longer itunes runs.
Nightly syncing actually worked better using the jailbreak wifi sync tool than it does using the official apple solution, which is disappointing to say the least.
It doesn't help that iTunes seems to have a memory leak issue as well. After days of running it is eating up gigs of RAM for no apparent reason. I close it and reopen it and its back down to a few hundred megs again. But after a few days its back up to 3-4 gigs again. All the while all it did is fail to sync on a nightly basis.
iTunes has always been a pretty serious fail for a windows app, but it seems like lately Apple believes that windows users (which account for more iPhone/ipod/ipad users than osX users) are not important.
I am hoping the 10.6.3 build fixes this error message popup problem. The other issues I have dealt with forever. Maybe one day Apple will actually start acting like the company everyone believes them to be and fix these problems and release software that just works (which is of course their old marketing campaign, which they have long since abandoned).