First off, you pretty much have to install Fallout via this method on new operating systems.
http://www.nma-fallout.com/article.php?id=1593
I do this with each new install of the game.
As for the black screen thing, that's a common problem, although it shouldn't be happening consistently, bringing up your PipBoy (to rest, etc.) should fix the problem by clearing the screen. This happens to me a lot as well, but only within hours of gaming, not every few minutes as you're making it sound.
You might want to check this out.
http://www.nma-fallout.com/forum/viewtopic.php?t=5061
Read a bit in the first post to correct the problem, it was never severe with me so I always just stuck to refreshing the screen by opening up my PipBoy.