Take the controller apart and clean the conductive rubber pad on the underside of the run button with an alcohol-dampened q-tip. Actually, do this to all of the buttons while you're in there. Over time, the rubber gets oxidized and no longer makes good contact with the PCB. I would also clean all of the button contact points on the PCB with a white eraser.
At least for me, this happens to all controllers. We just don't notice that over time we have to push down a little harder on the buttons.