I think I had some progress on this issue a few days ago after Apple released Aperture 3.4.1. The problems were definitely caused by iPhoto 9.4, and I use iPhoto on my library a lot more than I open it with Aperture, but they do interrelate because of the unified photo library now. Actually after fixing the grayed out issue because of the stupid ampersand in the slideshow music (see link earlier in this thread), I had a major issue with iTunes showing a faulty list of photo events on the Photos tab of my iOS devices, which affecting my photo syncing. But after installing the update to Aperture 3.4.1 this past week, closing iTunes, running Aperture, closing Aperture, then relaunching iTunes, the photo Events list in iTunes went back to normal and I think everything synced correctly to my iPhone and iPad. Need to verify a bit more, but am not near my MacBook Pro for a few days.
Sorry I can't be more definite, but if you have Aperture installed (whether you use it or not) I would run the update to 3.4.1 from the App Store immediately with the steps above and see if it helps some or all of your issues.
Interesting that there hasn't been any update to iPhoto 9.4 yet. I remember Apple introducing a very similar set of syncing problems back in iPhoto 9.0 or 9.2 or something, and the .1 update after that fixed it, but was very frustrating. Now the déjà vu of that issue is even more maddening.
Everyone report a bug in iPhoto.... Remember that Apple doesn't use this forum to gain information about bugs.