By far, one of the most irritating problems ever. Period. This problem's been plaguing me for weeks. Jump off a cliff and land in a fire.
I've got two totally separate sky boxes, and I can see func_walls through them. Now vis should be blocking them, right? Well it's not, and that's the damn problem. This is the general idea: Here's what I see from the bottom box, looking up: And here's what I see looking down from the top box: BUT WAIT, it gets better, because the only entities that are showing through the sky are func_walls. And some of the func_walls aren't shown through the sky. Things that don't fix this problem:
-Running full vis
-Moving the top to the bottom, or vice versa
-Using a hint brush to block vis between the two boxes
-Putting a normal brush between the two boxes, either inside or outside the sky