I'm playing Fallout New Vegas and I noticed at one point in my game recently the game all of the sudden got very choppy and the FPS has taken a huge down swing.
I had a hunch it might just be that game save so I made a new game and sure enough the new game runs just fine. So it's specific to just this game save. I did all my modding for this file well before the drop occurred.
Though to be fair, I had something like what you described after I fiddled with a few d3d9.dlls (Placed in FNV's folder, where the .exe is. For performance and bug remedies), saved, got choppiness, started new save, choppiness there.
Replaced d3d9.dll, reloaded old save. Choppiness there. Started new save, no choppiness.
Perhaps you fiddled with a d3d9.dll? Or perhaps you just had a mod that spawned a gajillion NPCs at the cell you are at, so it made your computer struggle and squirm.