Does the problem go away if you sync less photos, maybe a few albums? Does it go away if you free up more space on your iPhone (the pics don't take up the same amount of space on the iPhone because they are optimized)?
If it keeps happening, give this a shot -> iPhoto 6 and later: Rebuilding the iPhoto library
I have had the same problem with syncing to my iPad. I would select the albums I wanted to sync, it would show the correct number of photos in iTunes, then would only sync a few of the photos in the album. I tried everything I could think of (syncing without the albums then syncing with them again, moving pictures to different albums, etc.) and still had some photos that refulsed to sync. I finally de-seleted the albums, and selected the events that had those photos instead. This seemed to work. But not the best solution....
I have seen some threads where folks are moving from iPhoto to Apeture and that certainly would be another option. I am planning on doing that later this summer.....
Not really a solution, but thought I would share what I knew about this with you!
I'm having the same problem after rebuilding the hard drive from scratch this past weekend, only some of the photos in my iPhoto library sync. I have an old 32GB iPhone 3GS with 6GB free running iOS 6.1.2 syncing with iTunes 11 and iPhoto 09 and OSx 10.7.5. Before reloading the OS on my Mac there was no problem syncing all of the photos in my iPhoto library. I hope someone can help figure out this problem.