polyphony?

Im sequencing my supernova synth with the mpc. Ive got drums coming from the synth, and some other stuff on top. Thers a big bass line which sounded quite good. Then I put a bit of organ in the middle and now the bass sounds like it comes in and out a bit.Its all sitting nicely and then suddenly one of the bass notes comes out real strong and sounds out of place like its been hiding all the time and then it got a bit of breathing space and just pops out. Could this be to do with my synths polyphony. Or is there a setting on the mpc for polyphony Not a major problem. Just a bit annoying.

Yes it is a polyphony issue, you probably got some low end on your other samples that you didn't realize, so now that its all being layered together, you can hear the amplification of the bass. Filter those samples or eq them when you sample something.