Hi Nick,
I remember I had problems parking my Astro-Physics mount with the SkyX, so I wonder if you problems might be related to parking. As the mount doesn’t actually need to be parked I simply slew to a safe position and then turn it off. Of course your pointing problem might be something different but I thought I’d mention it.
Other possibilities to check are whether your location is set to come from the hand controller or the computer.
I’ve never pointed at Polaris as it is not a good star to use for syncing the telescope position. You have good latitude information but the longitude precision is about as bad as it could be as a tiny movement gives a massive shift in longitude.
Good luck, I’m sure you will get there.
Andy