Did your file play in VirtualDub? I will ask again :) Is it possible for me to acquire this problem file?
It is not easy to determine the problem over a text-based communication system. It would take – I dunno – maybe over a month to try out all options I could in an hour.
Edit:
I have not used AVIMedic and don't know what does it mean by "bad header". Did you select Matroska upon saving in VirtualDubMod? As I said before, maybe (depending on how bad the header is) mkvmerge/MMG is be able to recreate a valid MKV file from your AVI.
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