I have been trying to play Fallout 3 with mods for a couple of days now but they never seem to work. I am using Mod Organizer to keep most of my fallout 3 folder untouched. However whenever i launch the game there is not one of the mods that i have in the game. I also get another error when launching FOSE from my Mod Organizer which is "There is already a instance of Fallout 3 running" it then crashes a few seconds later.

Could someone please help me fix this problem?

I do not use Mod Organizer.

Sounds to me that you are not installing mods correctly in MO.

I did it exactly the same as i did with Skyrim which worked fine but this one is not working at all :/