I've been exclusively using the official Module Builder system. It doesn't directly interact with the files used by the game when editing, it only writes to them when you run the build batch file. So I don't see that as being a problem here.
Next time it crashes on me I'll try to make note of the error message. My LCD is dying though and shows a jittery fragmented screen at the resolution which the BSOD puts the system at, so dunno what I'll be able to read of it.
EDIT: Last time it crashed, it gave a Stop error at address 7f (I think) with the file splitter.sys indicated. I found that file and it is the "Microsoft Kernel Audio Splitter".
In case my audio card might have something to do with the problem, I'm using an Audigy 2 Platinum.
EDIT 2: I thought about it, and I usually have WinAmp running in the background even when I'm running M&B... maybe they're not playing nice. Haven't had a similar problem with any other game, though.
EDIT 3: Haven't had it crash on exit so far as long as I make sure WinAmp is not open when I exit M&B. So that seems to be my issue. Not sure now what the culprit is (probably some weak spot in Creative's drivers), but at least I seem to have found a way to prevent the BSOD.