For anyone still looking to solve this problem (I was, and had to work it out for myself in the long run from distantly-remember manual configurations of Dosbox) what you need to do is this:
find "dosboxSC3.conf" in your Star Control 3 directory and open it with notepad.
Find "cycles=max" and change cycles to a number. 3000 is a good place to start; it depends on your system so you will have to experiment to find what works for you (ctrl+F11 and ctrl+F12 will raise and lower, respectively, the cycles by 1000 while playing. Once you find the sweet spot you will still need to edit it into the conf manually)
Hope this helps!