Happened twice to me the first time I set up my iPhone 4.
Pain. Sorry it happened. Not sure what the fix is. But after doing it twice - I sync'd twice before disconnecting my iPhone and never had the problem again. I wonder if the "backup" was somehow corrupted originally.
Did you make the folders, organize the apps on the iPhone itself or through the iTunes interface? I haven't had this exact issue occur to me before but iTunes has taken things out of folders that had been in folders before the sync...
it's only happened to me whilst i've been sync-ing and messing with folders at same time, learnt to wait until it's finished copying or syncing before messing with folders
Any chance you're running an old version of iTunes? I had this issue back when I was trying out the beta of 4.0 because Apple didn't release an updated version of iTunes that could properly handle folders until 4.0 went public.
I was using 9.2 so i thought i had the most current one. However, the newest was 9.2.1. i downloaded that...and hope for the best...if anyone else has this problem, please post it too....