A real longshot (but simple): In the midi settings window there are a couple of switches relating to local on/off. Does toggling them make any difference?

At this point, might be worthwhile to test the controller completely independently of BB, with a utility like MidiOx. Oh, wait, the controller works with other music software? Hmm, this is a toughie. Maybe fire up BB, but set it to no midi input, then run it into MidiOx while BB is running. Just to rule out that there's nothing in the BB environment causing the issue.

Good luck. -Ron