I had this issue when I first got my 2500, and being inexperienced with MPC's, I just used it in mono for a while. But I did end up fixing it:
I took the casing off the MPC (take off the side pieces then the top plate), what I found is that the connection at the top right near the main volume pot was just not plugged in properly. I unplugged it and replugged it in properly and voila, both channels working from the stereo outs and the headphones.
Hopefully this helps!