Hi Niall
After you do your polar alignment, you need to re-do your Synscan alignment, because you have moved your mount in azimuth and altitude for your polar alignment from the original position of the Synscan alignment. This is why your Synscan is telling you it is off by several degrees. Re-doing your Synscan alignment will of course, not change your polar alignment because you do not touch your altitude and azimuth adjusters for a Synscan alignment.