Solved this problem for myself
Had the exact same problem after updating my iphone 4 to iOS 4.1. Interestingly, it'd sync certain albums, but not others.
Previous to the update, I had no problems syncing my aperture photo albums.
Tried reinstalling itunes 10.0 (had just installed 10.0.1 too). Didn't help.
Eventually it dawned on me that I had just added 4 photos to a smart album around the same time that the sync didn't work.
Since it was just 4 pictures, I removed them from the smart album, and it sync'd fine!
Then re-added them one at a time back to the album... syncing in between each add. Eventually found the offending photos. Just "made duplicates" of the offending photos via Aperture's "Make Duplicate from this Version" (or something like that). Added the newly-made duplicates to the smart album... boom.
I guess if you don't want to go through the hassle of sifting through a large album, you could just select them all and duplicate them all into another album, then sync the new album.
Hope this helps!