When REC w/count-in Pyramid starts early on 3rd beat

The brain of my system is an MPC1000 with Pyramid. The only issue I have run into is that when I have the MPC set with a 4beat count-in in record mode. The Pyramid will start playing on beat 3 and so then it’s out of sync with my MPC while I’m trying to record. It works fine if I don’t do a count-in on the MPC. Or if I’m just playing from the MPC everything syncs starts fine. Any ideas how I can fix this?