The problem might be auto settings on the scanner. If you're scanning different sections of the same negative, the scanner program will adjust based on the portion of the negative it's looking at. So it comes up with a different exposures. Then when you stitch, the two sides don;t match.
Try setting the scanner to make no adjustments during the scan at all. No sharpening, no exposure, nothing. Then either stitch before making changes in LR. Or make exactly the same changes on both sides in LR and then stitch. See what happens.
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