^^^I made mention about it more on the back end rather than the initial issue itself. Then there's other factors that could be the cause.
First, I'd look at the other hardware pieces that play a part in syncing everything together. What s/c's are being used? Any external midi routers being used other than the basic one in, one out config found on the s/c. Have you tried alternating between midi time code and midiclock on the mpc?
Have the drivers been updated or any hardware firmware updates done pertaining to any of the core components of the system?
Could be a number of things, or it could be just one. What's being used if you don't mind me asking?
MPC 4000
SSL Fusion
Roland JV1080
Ensoniq ASR10
Pioneer XDJ RX2
Korg Triton Rack
Kurzweil K2500RS
MiniMoog Voyager
Yamaha Montage 7
Yamaha Motif ES Rack
UA Apollo X8 Interface
Tascam DM4800/DA3000