Did you read the manual? did you check the settings on the MPC?
I guess you are using Q-link slider set to level or velocity to mute yes?
Cos that is the only way I can see you doing this.
I would recommend you actually just use a separate track for each sound, so track one for drums, track two is your break. Then use the mute screen, cos that is what it is for.
Now another way to approach this is using solo to, so if you have the sounds on separate tracks you can use solo to hear only one track and unsolo to hear all of them.
I indeed use footswitch for many functions, depending on what i do, though I have more options as I use OS3.
So if you actually do above you can change tracks in solo with footswitch, but besides that there is no real option of mute via footswitch.
That is what mute screen is for really.