The MIDI support in _all_ the emulators I've seen has been fairly... not-great... overall. I should look again but I remember reading through the source for Aranym around this and being pretty disappointed.
I've used STEEM to run Dr T's fairly extensively, with Midi I/O routed to either VSTHost or Reaper running as a midi rack, using loopMIDI and never really had a problem other than the occasion where I forget which way is in and out and end up with loopMIDI disabling ports due to feedback loops.
Must... resist... temptation... to write my own