I've had this problem now a couple of times: the audio is absent for the first few seconds of the first video track, then kicks in in-sync. There is no audio track on the main menu, so this would be the first audio on the DVD. If I go to a different track, or back to the menu, then come back to track 1 the audio plays fine. I'm using AIFF audio.
I believe the last time I had this problem I converted the audio to AC3 and it went away, but I'd like to know what's going on. Any ideas?