@keenmaster486 I'm pretty much out of ideas at the moment (and can't find a T41 to test with).
If you play a wav file with media player, and then start a DOS Prompt, is audio still playing normally? What about when you start a DOS game?

Please also install the A04.1 attached in this post. You can adjust buffer= in the .ini (needs a system reboot to apply). Try adjusting that and see if it makes any difference.

@stanwebber can you also try the attached version? First, without any changes, see if the MIDI stutters are gone. Then, in the .ini file, set priority to realtime instead of auto and reboot. Retest if the first note during FM playback is still messed up. Also retest MIDI as well.

Thanks for the Sysinternals process explorer tip, I will use that!