i don't know of any camera whose sensor is sensitive to the orientation of the camera... and although the image is formed upside-down on the sensor relative to the pre-meridian flip image, the sensor pixels themselves don't move. so the meridian flip should have no effect on whether or not you can successfully calibrate an image. even your flats will be the same pre-and post meridian flip unless you use a rotator to rotate the camera 180 degrees after the meridian flip.
also StarAlignment should have no problem with images that are rotated...
there must be some other problem going on here. can you post some of the problem frames together with your calibration masters?
rob