Today I downloaded the latest dev build of gzdoom (gzdoom-x64-g2.2pre-1403-g11cd38f), because 64 bits, and suddenly this "window" appears in this specific part of the level when looked from this angle, when I get close to it, it dissappears. I deleted my old config file to start fresh and no mods where loaded, I don't remember the exact build I was using before, but it could not have been further back than a week or so (I play doom a lot).

when I get close:
