I don't think this will show any problem if your PHD run calibrates - but try downloading GPINTCheck from Shoestring astronomy - and manually slew in all four directions to command guide instructions are reaching the mount / hand controller frioomyour PC.
One other small things I know if I calibrate then do a large slew, say greater than 60 degress, I'm probably best of to force a calibration again - less I see exactly what you described - PHD works against the mounts tracking!
Craig at stark-labs is pretty good; no actually he's excellent. See what he says and it might help to post all your PHD setting here - all of them!
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