Brinnmilo said:
Have you tried downloading a Large Address Aware mod? I struggled with FO and TES games for a long time until I got their respective LAA mods.
I'm not sure it will help, I'm pretty sure if it would then JesterRaiin would have had something to say about it, could be worth a try though.
LAA allows access to more memory, capped by default. However our fellow here stated that
"My computer isn't made for gaming and so cannot run high spec games" - i don't think his system has more than 4 Gb of RAM.
Then again, i would be fool to disregard something. Every advice counts.

You may try this :
http://www.skyrimnexus.com/downloads/file.php?id=3211
and this :
http://www.skyrimnexus.com/downloads/file.php?id=4192
Who knows, who knows...
And one more thing. Run Falout3 launcher. Disable everything. Select lowest quality of everything. Select lowest resolution (800x600 ?). Exit launcher, and statrt the game in windowd mode.
This thing infuriate me, because i know i had exactly the same problem at some point and i resolved it by doing something very easy... Yet i forgot what it was. :|