In radiant, all of my textures/terrains show up fine, lighting is great, but when I run the map, I have no walls, ground, floor, etc. All models, fx, structs, etc are still there. The only other thing not working is that I can't knife zombies, and they can't hit me. Shooting them works fine, but that's about it.

When compiling/linking, I get there error:
WARNING: NavVolume generation is skipped. Flying units might not behave correctly. This might be due to there is no nav_volume brush in the level, or the generation is skipped purposely by skipping -navvolume option.

However, from what I've read, this shouldn't make a difference. What am I doing wrong?

I have this same problem and it's very depressing. Can someone please help us find a solution? Same issue: Radiant is absolutely fine whilst modifying things etc. but when you go ingame the textures for all floors, walls and ceilings are invisible. What have we done to fuck this up?

I had the problem once. it ended up being something to do with buggering up the link to one of the files when you make the map. Everything except models ended up invisible.

I ended up creating another new map.

I resized umbra, fpstool, sun boxes and recreated the skybox to accommodate my map. I deleted the floor, the little wall and the reflection node and pasted my map contents into the middle. I moved the spawns in the middle of my map, the global intermission above and angled down, then I re-saved it as a new map andrecompiled.....and it worked.
I'm still not entirely sure what caused it, but I have a suspicion that it's got something to do with the sun relative to 0,0,0.
I.E. center of map being centre on XYZ axis'.