Got this problem first time, i have had FNV on win xp, now I have win7, I don't have any mods that interfeers with rooms and locations. Problem occurs in Hidden Valley Bunker and Kings School :C
That or cache-ing. If there are too many objects in a load zone and no room markers you get the game randomly deciding which things to load and which not. Likely its a modded interrior cell without Room markers.
Experienced the same with the kitchen in the Ultra Luxe once - on Win Vista. Now I am running Win 7 and haven't experienced it. I think my computer at the time had problems handling it. Not sure why though.
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Which version would that be then?