I have a 40GB .mp4 file that has no issues when viewing in windows media player.
When I place it in the Magix arranger, the audio is synced up fine.
When I start moving the movie around, or start cutting it up, the audio gets de-synced. I found that after I move or snip something, the video portion skips/backtracks a couple of seconds at what seems to be a random point, but the audio doesn't do the same. This leaves the entire video out of sync with the audio.
This only became an issue AFTER I updated Magix to the latest version.