I've been an owner of the GOTY edition for the PS3 for over a year now. I've not been trying all this time to get it to work right...mostly due to frustration caused by my nerd rage...but I've been tinkering with different methods, and either I got lucky or I found something.
There are different methods to how people try to "fix" this game. Some believe it to be fixable through options. Me, I think it's a gameplay issue. This, to me, explains why some have problems while other do not. It's about how you play the game.
The thing to keep in mind is that Fo3 wants to keep track of everything. Rememeber that school you cleared out? Yeah, it's keeping track of that. You need to keep it simple.
While the PS3 has the ability to run Fo3 awesome, it's a port. For the PS3 to run Fo3 the way it should, we're talking about them basicly creating an entire new game. So, yeah, it's a software issue, but one you can work around.