Playing Agrarian Skies 2, the manaseer monocle shows a gray box for a flower's area instead of the intended colorful semi-transparent one that's supposed to be there.

Press F7 to turn off the NEI display.

Thanks, that worked.
Is this something that can be fixed? (I'm not familiar with rendering, so I don't really know)

This is a problem with NEI not properly resetting GL flags they use.