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This kind of timing problem is common, unfortunately.
Here's a simple test you can do that will give you a little data about your MIDI inteface. Make (by hand, using say a grid editor) a track of quarter notes that are exactly aligned on the beat. Attach a MIDI cable from the MIDI OUT of your interface to the MIDI IN. Record a new track by playing the track you created out of the interface and back into itself. Now pull the two tracks up side-by-side in some kind of low-level event editor where you can see the note timing in detail. You will probably see that the start times not only do not line up, but that they are all over the place in the second track -- sometimes a few ticks earlier than the original, sometimes a few ticks later, etc. This is MIDI jitter.
Some interfaces are better than others about this. But it takes some work to find a combination that matches the MPC's timing. I have an MPC4000, and I settled on RME Firefaces as having the lowest jitter of the Firewire interfaces I was able to test.
Good luck,
-synthoid
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