Please do this for me again, strictly in this order.
1. Go to the setup menu and make sure "Load last session at power up" is disabled.
2. Go to the desktop and nuke every Startup session in any folder whatsoever (Flush down toilet). Check every folder. Leave no turn unstoned.
3. Shut the poor little darlin' down.
4. Reboot.
5. Stick your MPC in channels 1 & 2.
6. Assign input channels 1 & 2 to the L/R Mix Bus.
I'm of the opinion that you accidentally have channel patches engaged or pre/post channel inserts engaged. The above procedure will get you back to basics.
Peter