MeGUI: Producing corrupt files. Suspect MKVMerge.

[Sivar]

I am trying to back up movies (from DVDs which work fine) and have run into a problem with several of them.
The resulting file ends up being small (a little larger than the encoded MP3) and corrupt.
This started just in the last 5 weeks or so, but may be related to the movies encoding rather than the version of a tool that comes with MeGUI.

The log (complete file attached) repeatedly says:
[Warning] A warning occurred: Warning:

'D:\path\to\movies\movieName_Video_0.264' track 0: This MPEG audio track contains 2 bytes of non-MP3 data which were skipped. The audio/video synchronization may have been lost.

(italic parts change)

I use the 1-click encoder and choose a VOB file and encode it with fairly slow 2-pass settings. The problem occurs whether I am transcoding the audio to MP3 or simply adding the original AC3 or DTS track, so I don't think it has anything to do with MP3.

It seems to be similar to the problem this guy is having:

http://forum.doom9.org/showthread.php?t=145881

He suspects that MKVMerge thinks the video file is actually an MP3. Why it would think that, I am unsure.

With at least one of the movies, I got a good encoding in CRF mode, so I think the DVD rips are fine.

How can I fix this or otherwise get working MKV files? TIA.