Hi Damon,
I've had similar problems with MIDI on NT. Apparently, when Pd exits "abnormally" (i.e. when it crashes or when you stop it with a control-C) some drivers fail to notice this and to close the MIDI ports. It's all the more frustrating because all the MIDI-relevant functions in NT require you to open the port first; so there's no way even to write a program to clean up the mess (and I've tried.)
I've also got audio problems on one NT machine; I seem to be able to address one audio device but not the second one on my machine. Yes, the offending card is a soundblaster.
I've actually _never_ got reliable MIDI output from a soundblaster, come to think of it. Have any other PD-ers?
cheers Miller