I think I ran into similar problems running the MPC in plug in mode and eventually abandoned the idea.
However, that doesn't mean the two can't work harmoniously. Indded I have the MPC routed into Reaper and using Reaper as a glorified mega mixer.
Check this thread for the details on how to make that happen. I thoroughly recommend it and will tell you this. The MPC Ren takes on a whole new level of existence when it's routed through a DAW (not as a plug in).
viewtopic.php?f=36&t=173318That thread and the information contained within changed my world and made me see the Ren (& Reaper) through new eyes!!