In my case the problems were caused by:
1. Incorrect brain settings after the PHD software upgrade (along the lines suggested by Marc)
2. I changed to OAG and therefore a longer focal length. Again the brain settings needed to be updated.
When I had the incorrect settings I was seeing some very weird behaviour (refer attached - image scale 0.66 arc sec / pixel)
With the new settings, the problems have gone away. One key change was to reduce the calibration step size - the calibration was happening too quickly and this is what caused the random results after each calibration.
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