Do you have the stock head unit or an aftermarket? Clearly there is problem in the wiring between the head unit and speakers. If it's an aftermarket head unit (radio), I'd start my checking how the unit wired in. When I installed my Sony unit, I was able to find an adapter so I didn't have to splice any wires, but I have had to cut off the stock plug and splice on a new plug to fit the head unit on other vehicles.
OR maybe the balance control shut off that side!