This is because when the game is launched via Steam, it opens the launcher first, which overwrites your Fallout.ini file with the contents of the Fallout_default.ini file, along with your launcher settings.
(Note: In Fallout New Vegas, Most tweaks which would normally go in the Fallout.ini file in Fallout 3 actually need to be made in the Fallout_default.ini file found under the \Program Files (x86)\Steam\steamapps\common\fallout new vegas directory in Fallout: New Vegas. Open up the fallout.ini file in: My Documents\My Games\Fallout3 I haven't had it freeze once since I did this several days ago.
You can force the game to only use two of them and it will stop the freezing. The game engine has some issues with processors that have more than 2 cores. Please Note: Even though this was written with Fallout 3 in mind, it also works for Fallout New Vegas. If you have a multi-core machine, you may want to try these instructions: Fallout 3 (and New Vegas): Video/Display Freezes, sound keeps going
