MIDI Thru stops working after sequence playback stops

[kelcarpenter]

I have encountered a bizarre issue with external midi. Here is my setup, followed by the issue:

ProTools 10.3.9
Digi 002 Rack
Mac Pro 5,1 12-core running OSX 10.8
Korg Micro Kontrol 49 as controller via USB
External keyboard, in this case Yamaha MOXF6, although this issue exists with any external keyboard or module

I have a midi track output set to Avid 002 Rack, Port 2, Ch. 1
This has midi data on it, so when I hit play the sequence, it sends the midi to the external device.

HOWEVER, when I set the track on record and play from my controller live, nothing gets sent to the external midi device.

Yes, I have Midi Thru enabled.

Here is the BIZARRE thing: If I go to my Audio Midi Setup utility and hit Rescan Midi, suddenly everything works! The midi data played live from my controller successfully gets sent through to my external device, but as soon as I play the sequence (i.e. hit play from the transport), live midi through no longer works. So I have to go back and do another Rescan Midi, then it works again, until after the next time I play back my sequence.

To reiterate, a midi performance (sequence) plays back fine. But if I try to play live, it doesn't work, unless I use Rescan Midi in the Audio Midi setup, at which point it works until after the next time I play back the sequence, meaning I have to go back to Audio Midi and do another rescan.

I have searched the threads for this issue, but have found nothing specifically with this issue. Any ideas?

p.s. This issue is the same if I connect the controller via Midi as opposed to USB