I think this might be my fault. See
this bug report.
I was trying to bring the overall volume level in line with other music drivers and sound effects. (If you've still got an old copy of scummvm around, go to the bar on Scabb and listen to the difference between the music in the background and the sound effect of the bartender spitting. Compare the results of using the Adlib driver versus the MT-32 driver.)
I noticed the crackling when I was testing my change, but only at fairly high volumes. At 192, say, the problem goes away; as this is the default, I didn't worry too much about it. Try setting the volume lower, see if that helps.
As a side note, I'm fairly certain this has to do with the reverb in the MT32 we're trying to emulate; this problem is especially bad when the music is loudest (for example, when LeChuck is moving around). What's most likely happening is that sample overflows and what should be a very large value is actually a very small one. It makes me wonder if perhaps the MT32 author saw this problem and was intentionally shifting by an extra bit. I still think the change was worthwhile, however, as the problem (so far as I've been able to diagnose it) is easily correctable and this brings the MT32 volume closer to the other music drivers' volumes.