I doubt there's anything related to the scanner that you could do. It's simply the angle of the light reflecting off the plastic.
One suggestion may be scanning within the lid closed. Not sure if it will help, but that's what I do and I never had a problem with reflections. I also think the deep black border makes the scans look better.
If that doesn't work, you could also try "scanning" the card using a smartphone. I doubt you'll get the same resolution, but phones now do have that feature (it will look like a scan, not a photo, even though it is created with the camera).
Otherwise, perhaps something can be done in post-processing if you are familiar with image editing software.
-Corey
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