I believe that I have found the problem here. The problem is that the video track extracted by mkvextract is of a file type that any2dvd doesn't know how to handle. I have had a similar problem and when I did, I tried running the command:
file foo.avi
on the extracted video file and it returned something like this:
foo.avi: JVT NAL sequence, H.264 video @ L 51
I am unable to play...
2007-12-11 07:03:30 UTC in any2dvd