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Cut a section through your scope box and make sure its base cuts through the levels.
Other reasons are:
Crop Region may be Rotated manually. Some people do this instead of applying Project North or True North.
Crop Region>Edit Crop Region may be manually rotated. (individual lines in Sketch Mode)
Corp Region>Edit Crop Region may not be an exact rectangle or square
Solution is to click on 'Reset Crop'. (Contextual Tab)