Firstly... I have submitted a bug request to Apple (
http://www.apple.com/feedback/iphone.html). I think everyone who is experiencing this problem should do so.
This is a widely recognised issue on various forums and there has been no response from Apple (that I'm aware of) which is really disappointing. And this thread is NOT ANSWERED!!!
I have the problem with the latest firmware 2.2 and had it with 2.1. I've "manually managed music" as well as trying "sync checked songs only" but both have the same problem. It is sporadic in the sense that sometimes it's updated but most of the time it isn't.
I can't see why this should be so hard to fix. It's simply a case of the iPod/iPhone updating some sort of xml/DB with a count once half the song's been listened too and then syncing this to iTunes!!!
This is so frustrating!