Can't trigger midi devices since 6.4 upgrade

[Siberian]

Before upgrading from 5.3 with my digi 001, I had recorded some songs by using the internal protools midi clock to trigger an external midi compatible keyboard. I was able to trigger pre-programmed arpeggios from a Korg rinity keyboard, which synched up to the protools midi clock with no problem. I didn't record the tracks as midi data, but as audio, if that makes any sense.

NOW, after recently upgrading to 6.4, I can not seem to trigger anything from protools using the midi out. I don't know if I am missing something in the setup menu or what, but I am totally lost now. Was there any known midi bug or glitch in the upgrade, or something that I need to enable or change in my global settings? Just for clarification, once again, I am not actually recording midi data, but using the midi time clock in protools to trigger a midi compatible external device, then I am running the audio outs from the keyboard into my audio ins on the digi001, and recording the sound as an audio track.

Sorry to sound like a noob, but can someone just post the basic setup checklist so I can use it as a starting point to trouble shoot my problem? I've gone through the manuals and can't seem to find the answer to this....

I have a gut feeling something got fubar when I upgraded to 6.4. Any ideas?

Thank you!