According to your description, it seems that you forget the 2nd and 3rd passes of the typesetting. Once your source file is compiled, you get a *.mx1 file. You have to use the binary musixflx (provided with MusiXTeX, otherwise compile the source) on this file to get a *.mx2 file. Then you can recompile your *.tex file and all should work fine.
Olivier
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