Star Control detects the MPU-401 interface in DOSBox, and uses it in preference to other sound devices; however it only supports an MT-32/LAPC-1 synth, and the instrument patches often don't sound right with GM synths. You can hook up a real MT-32, or use a special build of DOSBox that includes MT-32 emulation like MUNT, but otherwise you need to get StarCon to use another sound device. One way to do this is to disable the MPU-401 by typing "mpu401 none" at the prompt before running the game (or set mpu401=none in the conf file), forcing it to find another device, probably an Adlib or CMS. There are also command line parameters for selecting the sound device you want to use, consult your manual for those.

Edit: there is one other option for using a GM synth with games that think they're driving an MT-32. I have a MIDI file called MT32EMUL.MID that was included with Roland Sound Canvas synths; it remaps GM patches to be close to what an MT-32 uses, which is an improvement, but the sound is still not authentic, and of course any SYSEX messages a game uses won't work. I tried it with Star Control, and it actually works pretty well with the GM synth on my Audigy 2 ZS. Unfortunately, I can't post the remapper MIDI file because it is copyrighted by Roland.