Possibly related to this problem:
However, I don't think it's the same because it also effects local repositories. I encountered the problem above and tried to change all of the non-zero playcounts on my songs back to 1. When I did so, gtkpod changed all my ratings to 4, and I had to restore my iPod from backup to get it back to its previous state. Retesting found that doing a batch operation to change play counts changed ratings unpredictably, even on a local repository without the iPod conected.