Thanks Whatzup! Your suggestion worked perfectly and now my photos are syncing normally again every time.
In my case I didn't need to play around with any of the Smart Albums - Faces was the cause of my problem. I noticed that in iTunes under the Photos tab, when I chose the 'selected' option, there were people's names under faces that according to iTunes only had one photo assigned to them. In Aperture however, none of these people existed under Faces. Not sure if it was a coincidence or not, but all my problem names came from facebook! Perhaps the Aperture plug-in was the culprit?
Anyway, in Aperture I made sure a photo was assigned to each of the names from iTunes. Then, in Aperture I deleted the people that shouldn't have been there. After restarting iTunes, their names disapperaed from my list of Faces. Instead though, I found a duplicate name! I repeated the same process in Aperture. Interestingly, I noticed that the first name came from my address book and the second from facebook. Once I deleted the wrong version, the duplicate disappered in iTunes. Now, finally iTunes showed a correct list of faces!
Syncing all photos ever since has worked, even after adding and deleting photos in Aperture. Hope this helps and good luck everyone!
PS: I lodged a bug report with Apple but never heard back. Hmm.