Yup, I agree, I think what happened was when I was testing this I was doing it on an image from citra which was already flipped the right side up. So if you use the image viewer and load up an image from citra it will work properly.
This is what I get by default (With an image loaded in imageviewer):
I’ll have to see what should be done to have it sorted properly, because the whole reason I added HSM_DUALSCREEN_2ND_SCREEN_SIDES_CROP was to crop the bottom screen of the 3DS.
I also need to fix the Megabezel logo to appear in probably only the top screen when using dual screen instead of being split in the middle.