I think I have solved it, but cannot at this point say 100% what the issue was, as I broke the cardinal rule and changed more than one thing!
I have been attempting for the last two hours to start the polar alignment wizard to coincide with a patch of clearish sky, I must have attempted about thirty times just to get as far as the second capture, which is now working instantly, yay.
I eventually managed three consecutive full polar alignment wizards, getting closer and closer to zero each time, third one being 12 arcseconds off, which I think is acceptable!
I think the main problem, which I am still not sure if it should be a problem or not, is that I had my guide camera in my device profile set to Altair, and a second Altair driver in my AUX devices. The reason being I have two altair cameras, one which is used as a standard guider and the second used as a polemaster equivalent. The reason I did this is because I had come across a post where someone asked how to do almost exactly what I was doing, but the subtle difference being their cameras required different drivers.
In the past I have removed one of the cameras, but didn't think to remove the driver. Then tonight I removed the AUX Altair driver, and restarted Kstars and was surprised to see both cameras were still picked up.
I will try to prove this when I get another clear night (totally clouded over now), by adding the Altair back into the AUX devices.