although, i think you must be debayering your CR2 files, which you should not be doing. if the DSLR_RAW module is configured properly (pure raw), it will ignore the rotation metadata in the exif header. if DCRAW (DSLR_RAW) is allowed to debayer the files, i think it respects the rotation metadata.
calibration frames should not be debayered first, they should be kept in CFA format...
rob