To my trials VC1 is a little bit complicated than h264.
I think it is not related with the VC1 is interlaced.
If you are extracting video with eac3to and put into the mkv container (BTW eac3to uses Haali muxer which is the source of the issue) you will always live issues.
Extracting to VC1 instead of mkv will solve the problem;
please read this:
http://forum.doom9.org/showthread.ph...58#post1170058
best.
EDIT: The method i use:
http://forum.doom9.org/showthread.ph...90#post1137490
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