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The source extraction settings for "Tools->Image Link" vs. the automated calibration are separate. One is in "\Source Extraction\default.sxt" and the other is in "\Source Extraction\AutoPointingRun.sxt." If "Tools->Image Link" works well for you, then you can just copy default.sxt to AutoPointingRun.sxt. Or you can change the automated calibration source extraction settings via "TheSkyX->Telescope->Tpoint Add On->Calibration Run->Automated Calibration->Setup->Source Extraction Setup." The "Take Image and Link Photo" button in the same setup dialog is always a good thing to click on (and wait a few seconds for it to complete!) before starting the run.
Automated calibration already saves images in a separate directory regardless of whether or not you've set TheSkyX to save images. I don't recall if it's still doing this, but it was saving them twice, once in the "\Automated Calibration\" directory and again in your regular saved images directory tree. You might want to periodically clear out that "\Automated Calibration\" directory.
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