I don't have the factory amp, I have the bypass harness installed.
Either way I fixed the problem. The pins going from the aftermarket harness (the black square plug) were not lining up with the factory hookup in the dash.
You can see if you have the same problem by pulling the pins out of the aftermarket square connector and place them in the correct location in the factory connection. If the speakers now work, then the pins simply need to be bent to line up with the factory connection.
