I had an SNES controller with a start button issue too. Blackened a lot of erasers trying to clean it, but now it works (more) reliably.

Found my Model 1 Genesis controller and cleaned it, and after awhile the B button (which was bad) started working reliably... but then I found out the controller has a very sensitive left and right on the D-pad (I often try to shoot strait up or duck in Contra Hard Corps, and wind up moving sideways instead). Went back to using the one with the "loose" D-pad, where I know exactly what I'm pressing every time.

So... I guess the D-pads that are good for some games, aren't good for others.