Are you sure the CD and AM are working through all speakers or just throuhgh the centre one and you have the FM in "Normal" stereo mode so the centre speaker will not be used?

Assuming it is the Dolby setup, there is an amp under the driver's seat which drives the left/right channels but the centre dash speaker is driven directly from the head unit.

If you're losing all of the channels (centre included when in a mode it is used in) the head unit is probably at fault, if you lose the left/right but centre still works then it is probably the amp.