watched your video, and I'm not so sure why it would be doing that except for maybe a midi feedback loop. I didn't really follow closely what you were saying, but sometimes if this is the case, weird things start to happen. I'm now using an external midi in (8in/8out) box and it has helped to eliminate these issues. However I still use my audio interface(presonus firebox) to send the "start message" to the MPC. Maybe check the "syncronisation setup" in protools, (that's what it's called in cubase) and set the Computer to Masterclock, and have it going through your audio/interface. Also click on "always send start message" This is to make the MPC play when you hit play/record on protools. Hope this has helped you somehow.
GEAR: Moog Voyager, Roland Juno 106, Roland JX-3P, Hammond T211, MPC 1000, Sherman FilterBank 2, Korg Kaoss pad, Yorkville LS 800 P (for phat bass)