I noticed the same some time ago and did a bit of debugging it in PHD2 and it seemed to have something to do wit how the automatic restoration of the calibration is run after connecting INDI devices, the state is not what it expects yet and it occasionally skips or discards the calibration. You can see this by the red cal text in PHD2. Manually restoring the calibration via menu tools -> modify calibration -> restore calibration data... restores it for that session correctly however, but is annoying if you forget to check it when starting PHD2. However, automatic calibration restoration has worked fine for me again the last few days I've tried, and there was an update to how INDI device connection is handled in PHD2 so that might have fixed it.

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