It could be a coincidence, and it just became miscalibrated after time. OR... assuming your subs are high powered and pointing backwards, you are creating too much magnetic interference for the module that is located on the shelf in between the 6x9'*, most likely right above your subs. I could be wrong about the sub direction, I can't remember which way the poles point at the moment, so maybe yours are pointing up, but probably not if you had them installed by a shop. I messed up my compass trying to give it a fresh calibration two years ago when I only had about 300 watts in the trunk. My subs point up and didn't notice any change in the compass readout.
There are directions in the manual to calibrate it, although they may not work with the subs there. I suggest you have the system completely off when you do so. If that doesn't work, you may have to move the module (black box on underside of rear shelf directly between the 6x9'*) to a less magnetically exposed location, just make sure to orient the box in the same manner.