Turns out that JarateKing's CleanTF2plus makes certain textures like grates and windows invisible. I talked with RGL staff, and they said this isn't allowed (Here's proof of that), and would result in a full cheating ban. So to fix this, I made my own!
Here's the aptly named FlatTF2RGL, which keeps things legal by excluding affected textures. I also have a Pre-Compiled VPK for you to use. My version still works on sv_pure servers by keeping the "resized" option to flatten the textures to a 1x1 size.
Enjoy!
(The generator only works on Windows, sorry)