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error messages? often rotation in camera is an issue.. you take subs and the camera notes in the exif data a rotation to show which way the photo should be orientenedbut then you go inside to take flats and the carema is often oriented for normal phototaking so the software assumes subs are portrait oriented and flats landscape so you have dimension mismatches and no way to know which directio they should be rotated to match properly.
or maybe its something else, your post isnt very helpful with information like actual error messages.
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