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Have you checked the calibrated version of the files, Lewis? That can happen when calibration goes wrong and truncates data in an image.
For a problem like that I'd run BPP with Calibrate Only ticked, check the results look OK, and then run StarAlignment manually and tweak settings if needed.
I've rarely needed to adjust the StarAlignment settings but I have heard of cases where it was necessary to adjust Noise Reduction or other Star Detection parameters.
Cheers,
Rick.
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