I had also problems with the crop feature, I had a WMV that needed to be cropped, mkvmerge did not allow me to import wmv so I used Haali's DS muxer. The resulting mkv file played fine. Then I opened this file with mmg, entered the cropping, remuxed it. It would play jerky then and no matter what player I tried the crop didn't work. I ended up to reencode which didn't hurt much anyway.
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