http://forums.nexusmods.com/index.php?/ ... fallout-3/
Archive Invalidation is an important part of the first stages. It sets up the game to allow mods. Maybe that's what's not working.
As you install and add mods you'll start getting familiar of what's going on. You're basically adding the esp files to the data folder, textures and stuff to their folders (located in data folders). Well that's if the mods don't come in a easy to install FOMM package.
I'm not a computer guy but after getting my elbows in it, it still sucks but it makes sense. I think there's a better mod installer now. Try Nexus Mod Manager, I think it also works with Fallout 3. You just find the mod, click on "Download With Manager."
This will be the most important site for finding mods, tools, and utilities.
http://fallout3.nexusmods.com/
Nexus Mod Manager (it says skyrim but it works with fallout 3)
http://skyrim.nexusmods.com/content/modmanager/

Also what are your PC's specs?