Elcaro

Try going into your start menu then the Control Panel, look for something called device manager, open it, then open the human interface devices, you should find something with infrared in the title. Disable or uninstall it, after a while if you uninstalled it it will reinstall itself. Before it reinstalls itself open your game and try the (~)key again, it should work now. And you'll have to keep disabling/uninstalling that device each time you want to use the console. Hope this helps.

Or go to this wiki page(http://fallout.wikia.com/wiki/Console) to read more on the console and commands for Fallout 3