Thats the Creation Engine for you!
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.