Are you using a gemini II? If so that is likely the culprit. There is a known glitch when calibrating. It always occurs on north calibration, it's like the backlash never clears after an east/west calibration, and its intermittent. All you have to do is nudge the scope north a few pixels to kick start the north south calibration. Press the top direction button and phd engages again and completes the process.
Cheers
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