I don't actually have much experience working with these apps, but on a second reading of the problem, I realized I was thinking of a different problem(an external generator sending stuff from a serial port into the computer). The key to solving this one is just to get the MIDI data into the Windows MIDI mapper system.

If you have access to the app source you should be able to rewrite the code to use DirectSound or FluidSynth to play MIDI rather than touch the serial port.

If not, two dirty-hack options come to mind: you can loop the serial line's output back into the computer with a USB MIDI device(classically, MIDI goes over a 9-pin connection, presumably you already have a solution for serial-to-9-pin with the original setup) or you might be able to poll outgoing serial traffic and remap it with some code.