I tried the movies on different players. WMP , VLC and gXine on Linux. They're in sync on my desktop machine. And suddenly every movie I encode is in sync on my N800. My Linux System is fried because of a hd failure and I use puppy Linux for a couple of weeks. I'll have to get a real system back because I can't install stuff like media converter on puppy.
According to the date, I might have 1.31 installed on my windows box, already.