My last attempt ...
If you make any edits to your iTunes library (artwork addtions, tag edits, etc.) in between syncs, then that can disrupt playcount updates. Specifically, if you updated the songs in your library without re-syncing your iPhone, and then played those updated songs, they won't show a playcount update on the next sync*.
*One caveat ... the above has been true for every iPod I've owned, except for the Touch. Amazingly, I can make any tag change in my library, even go as far as change the name of a song, and the playcount from my Touch will still register on the next sync. This has not been the case with any of my other iPods, only with my Touch, so I assume the same may be the case for the iPhone.