Fixed by removing:
<score-instrument id="P1">
<instrument-name>Violin</instrument-name></score-instrument>
<midi-instrument id="P1">
<midi-channel>1</midi-channel>
<midi-program>1</midi-program>
<volume>80</volume>
<pan>0</pan></midi-instrument>
I guess I have to read the documentation for that again. http://www.musicxml.com/tutorial/percussion/multiple-instruments/