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I got a response back from Auriga Imaging. They indicate that if the sub exposures have the column defects/hot pixels in different areas of the image (achieved by pixel dithering between subs), they will still be successfully removed on a median (or sigma reject) combine function. So the image registration as such will not impact this. Two additional comments were made, take more subs and check dithering configuration.
I think on reflection, the latter has got me this time around. When I set up a imaging sequence in MaximDL, it keeps track of the dithering used. If you stop a sequence (which I did due to clouds), then start it again, dithering zeros (defaults) and starts from the same location again. Thus not all sub exposure defects were in different locations. The more subs you take the better this will be handled. I may hit some MaximDL forums to valid the dithering process.
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