Why does MKVToolNix cure my A/V sync issue?

[pooksahib]

I have an AVI file with packed bitstream MP3 audio and the movie plays fine on my PC. After running an avisynth script on it, however, the audio is out of sync. I made an MKVToolNix copy of the AVI file and ran my avisynth script on that - perfect result.

Making the MKVToolNix copy takes seconds which suggests there's no recoding taking place. So what does MKVToolnix actually do to make the movie behave with an avisynth script?

[ProWo]

Mkvtoolnix has remuxed your avi and rewritten the timestamps.

[pooksahib]

Thanks for that.