Hi thedutchgost,
This
http://www.vogons.org/viewtopic.php?f=7&t=35933&hilit=star+trek+judgement+rites&start=40#p328791 might solve your issue, though I believe the first link I gave had been updated with the fix.
I have the original CD collectors release so cant test this patch with the GOG version but dont see why it wouldnt work for both. If you cant get the original install working you could try manually changing the settings in TREK2.CFG. Settings that change when you select MT-32 instead of Soundblaster are (for me anyway):
"music=A002" (soundblaster) to "music=A004" (MT-32)
and
"setup=0,0,2,0,2,0,2,1" (soundblaster) to "setup=0,0,6,3,2,0,2,1" (MT-32)
along with "music_io=" needing to point to the interrupt address your MT-32 uses (330 seems to work best).
Over at
http://www.trekbbs.com/showthread.php?p=8582731 I have helped someone else who was having issues with the game hanging after he had applied the patch files (posts 24, 26, 27, 30). It ended up working for him by just using the updated exe from the archive and not worrying about the patched "DATA" and "FED" files as these only fix a general midi issue which is not needed for the MT-32 fix and seem to cause an hanging problem with some versions.