Do you tape the film to the mask or did you make the opening a tad larger than the film so the mask acts as a guide to position the film? The 4 x 5 mask that i got with the scanner has holes that are slightly smaller than the film size so I have to tape the film onto the mask and then put the mask (with film) over the locating pins. A little bit of a PITA, but not so hard. I'm pretty sure the scanner bed is ANR glass so should cause no issue with Newton's Rings - which seems to be your experience.
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