I've noticed this most often with converted mpeg transport streams. It seems to be worse with an increased number of video filters. The sync problem exists when playing the converted videos with mplayer on my computer, not just on an n770/n800.

EDIT:
If the material you're converting is at 24 fps ( film rate ) you may want to try a pulldown reversal filter like "-vf pullup" or "-vf softpulldown"