Like others have mentioned, don't put the card right against the scanner edge. I put another standard card against the edge as a spacer. You can crop it out later. A toploader or other relatively thick thing could cause the lid not to sit flat on the card your scanning, causing inconsistent shading or a shadow along the edge. A pretty small detail to be sure, but I'm weird like that. :-)
Also, like Billy Kingsley alluded to, it's sometimed good to experiment with lid open versus closed. I keep it closed for rounded cards, as well as die-cut cards, so the space shows as white rather than black or dark gray. Just my personal preference.
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