I wanted to come back to this thread to report back on what I have found out.

Thanks everyone for your explanations and advice, it was useful.

So basically, things are as follows:
PHD2 does do it 'better', but this is actually irrelevant because it partially masked the real issue.
The entire system was horribly unbalanced. While I am aware of 3D balancing and I had thought I had done this correct, this was incorrect. I had RA and DEC balanced, but any movement would cause both axis to run away in one direction or another.
The internal guider had a much harder time coping with this than PHD2, but again .. irrelevant. Both results were bad.
While I have not managed to perfectly balance the system, it is now much, much better behaved and the internal guider is managing reasonably well.

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