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During the calibration does the star move out and come back to the same spot, and then move out and come back again?
I found I had a similar problem to yours when I pointed 11deg west of south rather than east of south (ironically enough given you're trying to do alignment). In that case the steps in one direction couldn't keep up with the star movement through the viewfinder so the star went out and never came back. I continuously cranked up my step size (mistake) and when it did finally calibrate I ended up with unusable tracking.
When you turn all guiding off does your star move a lot in the PHD frame?
The other thing I found was good to debug was to select the RA / Dec overlay (can't remember what it's called exactly). But basically according to the guides I've read if it appears as a grid then it's good, but if it appears as a skew set of lines then your initial alignment is off (again doubt this is the case from what you're saying though).
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