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The problem in question only appears in very specific spots, and I'm not yet quite sure what causes it. Essentially, some walls will render entirely transparent through TROR layers, sometimes rendering the skybox in their place.

It is very noticeable in one the maps of Episode 3 of the AMC TC:

Classic Mode:

Polymost:

Bisection indicates this was caused by the following commit:

commit 421b54a8abb51e91cc539ec3a323e8581e2e05f7
Author: nukeykt <alexeytf2@gmail.com>
Date:   Thu Jan 28 12:58:52 2021 +0900

    Polymost: fix transparent floor/ceiling double drawing

 source/build/src/polymost.cpp | 32 ++++++++++++++++++++++++++++++++

Since the map in question consists of entirely custom textures, I extracted the portion of the map and plastered some Duke3D textures over it, as a test case. There's still a lot of HOM and it looks ugly as sin, but you can still observe the problem: _ejipt.map