SWR = standing wave ratio, or sometimes SWVR = standing wave voltage ratio, to differentiate between measuring power or voltage. Ideally your antenna should 'look like' 50 ohms; all the signal travels down the coax and into the antenna and the SWR = 1. If the antenna does not have a 50 ohm impedance, some energy is reflected back up the coax and into the transmitter, and the SWR will be greater than one. The higher the SWR, the worse the mismatch. Some transmitters do not like this, and may react by radiating spurious RF. If this gets into the autopilot electronics things may go wrong. That's the theory. It would only show up as the autopilot misbehaving during or after transmitting - you should see a correlation.