I'm new to the mpc2500 but last night I was experimenting with recording track mutings.
What I discovered was that recording track mutings work fine but what you are actually muting is the events rather than sound (which makes sense imho).
What this means is say you have a 1 bar sequence and one track in that sequence has a sound triggered right at the beginning of the bar, that sound is 1 bar long and set to one shot. Now if you play that sequence back looping, if you mute that track just after the sample has started playing it will continue to play until it finishes but then won't be triggered again until the track is unmuted.
Likewise, if you unmute the muted track just after the sample would've been triggered then you won't hear anything until the next time it is triggered.
I don't know if that's the problem you are having but it may be, hope that was of some use
