The only thing I can think of trying at this point is to see if using MIDIOx to check what's passing through which MIDI ports throws any light on things. It might be worth checking the events list as well if you've not already done so.

Other than that I've no suggestions at the moment. The one time I've seen something that resembles your description it was when I'd accidentally set up a MIDI feedback loop, but your problem may well be something quite different of course.