The only thing I can think that could be causing that is your laptop is sending a higher than usual voltage to the phone when charging and that causes the vibrator to start up. And you should call Sony in regards to that. If you have a multimeter you could try testing the voltage on the USB port to see if it spikes when charging.
The only other thing I can think of is that the phone shorts out when you pick it up(as humans produce/conduct electricity and the back of the phone is metal). So that would mean it only vibrates when holding it, not when placed on a table.
Current phone: Nokia Lumia 1020
R.I.P.: HTC Mozart, HTC HD2, HTC G1, Palm Pre