I tried using another gameport joystick with the same results. Anyway, I played one mission using the mouse, and I started getting the same choppiness in the sound, getting gradually worse. I quit DOSBox, restarted it and played another mission using mouse, this time with no problem with sound. I've noticed that Wing Commander has a strange urge to force Adlib for sound with DOSBox, even when I've disabled it in the DOSBox configuration file. Whatever I select when running install.exe through DOSBox, it doesn't really seem to change to configuration file. So I tried running the install program through Windows to set Sound Blaster, and setting the WC config file to read-only, but even that didn't stop it from using Adlib.
edit: Now this is interesting. When there isn't a joystick plugged in, Wing Commander has the firm opinion that there is a Sound Blaster, despite what I choose in the setup.
more edit: Tried slightly newer sound card drivers (figured that legacy emulation thingie might be causing troubles). Now WC identifies the sound card as Sound Blaster, but still the choppiness remains. It isn't just the music, but the game overall, I've noticed.