Leon, Sorry to hear about your troubles. There was a version of PHD which caused a lot of problems, I got caught with this one a while back and with an uninstall and reinstall of the latest version my troubles were over.
Polar alignment is worth a look but I have found PHD would work with A & E figures out around 200 - 200. It struggled a bit but still worked. What sort of A & E figures are you getting with a 2 or 3 star alignment?
The only other thing worth checking is that all the PHD setting are set to default settings.
Sorry I can't help more.
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