mplex only works on mpeg-based files, so of course it's going to fail if you try it with an .avi.
I've never used kino, so I can't tell you what's wrong, but if worse comes to worse, you can export to avi and then convert it to mpg with transcode or mencoder.
If you can give me some more details on exactly what you're trying to do, maybe I can help you work something out.
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