FireWarp

That's too bad . My only guess would be that hammer is somehow overwriting your custom compilation parameters. To check if that's true, compile vis on fast and compare it with normal settings. What fast compile does is that it actually checks whether or not the visleafs created by vbsp are correct and that's pretty much iit. Whilst on normal setting vvis performs portal flow correctly, making source cull parts of your map during gameplay. All of this means that fast vvis does pretty much NOTHING. Compiling without vvis shouldn't make any difference

@NihiL Did you change any of your skyboxes? I had the exact same problem but the steps I told you about fixed that for me.

Have you tried using normal mode? Although there isn't really a difference between expert and normal when it comes to vvis, but that might fix it.