There is no point in duplicating something that is already well supported on basically any platform (there are very good software synths around). Maybe try with yamaha synth, if it produces better result (and sound quality) on your machine. Btw. I also currently use Microsoft GS and have yet to encounter such problem with it.

If this appears with/after a specific game, it might be dosbox problem as well (like special (system/realtime) midi messages which shouldn't be sent out to MS GS).

It works after I restart DOSBox, so I'm sure DOSBox could internally reset the MIDI device (but then it has to know when to do this) - it just didn't happen with my old machine. Shame there's no tweak to make the MS GS 44kHz instead!

Well, it could even be a mpu-401 gltch (or unfinished midi/sysex etc.). Does it work when you set uart mode instead of intelligent? Maybe mpu401 reset should empty midi output buffer of dosbox as well.

Which game is it?

LSL1VGA says "Cannot initialise music hardware" when I choose Roland MT32 + Soundblaster. No such problems under my old system.

I just switched mpu401 from "intelligent" to "uart" and now music works in Larry. But I still get the problem where if I run Doom, and then run Underworld 2 for example, I get no music.

Just to be sure: what dosbox version are you using? Did you try it with
a fresh dosbox.conf?

0.65, and yes.

I tried to reproduce: ran Doom Demo set to "general midi" and then ultima underworld 2 set to MT-32 (and no digital sound). Both produced music.
Have yet to try with Larry1 vga.

Nothing works after I run Doom, other than Doom... ie. Hocus Pocus doesn't play MIDI either. If I do a "device=win32" between, it restores the sound.

One more attempt you can try:

After running Doom, execute:
device=none
device=win32

And see if you get anything. This should close and reopen windows MIDI device.
(Debug build would display log message about opening it, not sure about regular builds though.)

Anyway, for testing if there is any MIDI output, you can install something like MIDIYoke as default output device and route this to an analyser program (e.g. MIDI-OX from the same homepage) to check if dosbox actually outputs anything after running DOOM and also if this output is proper MIDI data, not garbage.