Problem
The engine seemed to be able or is able to map the parts of the surface to be partially transparent, not the entire thing. Initially Quake 2 engine allows to set trans33 and trans66 (33 / 66% of opacity) surface flags to make the surfaces partially transparent, but it apparently affects the whole thing. And so for some reason this got carried out into the game on some maps. Certain objects have a border due to not being completely transparent. It might have been due to some maps being recompiled while patching the game.
Solution
Enable alpha test on the partially transparent textures. That would not allow the selected surfaces to be partially transparent, but will at least get rid of the borders. Not ideal, but seems good enough as a workaround until the actual solution appears. This can be done by altering textureinfo.dat (/anoxdata/textures) and listing the textures having that issue under Alpha test section.
