Check that the dark brushes aren't duplicates. (ie. try to delete them, if they don't disappear at once then there was two inside each other which screws up light and stuff)
Well, running nobounce seems to do the trick, so I won't use bounce any more on this map. However, this may be because the map is freaking huge, I mean, aside from the areas that are playable, there are lots of margins, for example, check how long you fall before you die. And of course, the map must be sealed off from the limbo, so it's inside a huge room. Radiosity kind of didn't know what the hell to do with the thing. Also, there are no duplicate brushes. I'd know if there were any, because they're very likely to cancel each other out, making themselves invisible. Also, how do I fix the warpzones? They work, but don't show the other side.