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good start, the 40d is a nice camera, try shooting in RAW , then convert to tifs to stack and calibrate. you will find you have more flexibilty to push your processing.
i have had PHD do similar to me, usually ive left the manual guider in the guide slot from when i composed the shot, you could try calibrating at a higher speed (ie 1x or even 2x just to confirm signal is going through)
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