If you are sure that the panning is not the normal result of applying a stereo FX in your patch(es), then I would reflash the memory. Start the X3 in safe mode (hold down the right nav key while powering on) then run Line 6 Monkey and select the Flash Memory command.
What happens if you select the TUNER and put it in to BYPASS mode using the right hand rotary knob ?
Try deselecting / switching OFF all effect blocks, including AMP
If you've still got the problem even aftera full reset, then I would guess it's a repair needed I'm afraid ... ... :-(