I think the problem is that you have to keep the MIDI-track record-ready. Otherwise to application won't let pass MIDI data to the chosen output. The "emulated" outputs seem to the norm with PT on windows.
HTH,
/Dietz - Vienna Symphonic Library
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Sorry that I can't help you - I do a lot of mixes on ProTools, but never on Windows and hardly ever with "live"-MIDI, so I have no idea what these OS-specific issues with MIDI might be. - Usually, in the Windows-world, those things are pretty straight-forward ... :-/
I use ProTools 9 and MIR together on the same windows computer and it works great for me. Things I do is...in ProTools, midi in needs to be whatever your useing to input midi info and out needs to be LoopBe30 on whatever chanel (1-16) you want.Then in MIR when you open VI or any VSTi it has to be on the same chanel as your selected midi track in ProTools. In ProTool your midi track has to be record inabled. Thats all Ive ever done.Never had a problem. Hope this helps