I hope this helps someone.
I ran into problem similar to whats mentioned in this thread, where I would launch the game and would just get stuck in a loop with the launcher. Well it turns it if you start adding, removing, changing the location of your documents, and your library settings, the launcher loses track of where "My Games/Fallout 3/" Directory is, and doesn't seem to recreate it, just gets stuck in a loop.
So double check all those settings, change or move your "My Games/Fallout 3" directory and you should be good to go.