Remuxing generates an audio delay

[ChrisR34000]

Hi!

I hope this the right subforum for this issue:

I encoded the Aliens DVD (the second Aliens disc - commentary) from the quadrilogy boxset with MeGui to x264. The ac3 file was demuxed. When I try to remux, mkymerge gives me a warning that audio sync may have been lost and indeed, the sound is delayed from the middle of the video file. When I start the ac3 file externally with Media Player Classic, the sync is fine, however, I just can't seem to be able to remux properly.
Do you know a way to fix this?

Thanks,
Chris

Edit: Ac3fix does the job