Don't think the "not quite right polar alignment" is the problem Leon. I agree with Marc, try a 5 minute shot, tracking no guiding, and see how badly trailed it is. If it is at all.
Like has been mentioned maybe un-install, then re-install PHD.
Maybe, if you have it, try something like K# as well, it guides. If anyone you know has a guide camera, and laptop, try them on you scope/mount combo.
Gary
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