If the glass is too thick, you will get internal reflections off the beveled edges, the moveable masks are there to eliminate excess light spill onto the easel. Try moving them in a 1/4" or so and see if the problem still exists.

If the glass is too thick, they may not sit flat against the whole surface of the negative when the carrier is in the enlarger, causing all sorts of weird abnormalities.

I'm just throwing out ideas for you to check, not having ever see that model of enlarger, but have seen may weird things from poorly modified ones.