I use many mods, and they all work fine. I don't have this problem with any mods that I've downloaded from SkyrimNexus. (Or maybe I do? I don't usually use coc to go to cells added by mods that have mod-added actors in them...)
In order to test, I disabled all mods (everything except for Skyrim.esm, Update.esm, and Live Another Life.esp, because I don't want to spend half an hour to start a new game to test) and started a new game, and the problem persists. Here are ASI and DLL files i have in case it's relevant. They're the only things other than plugin files that should be able to make any difference, right?
iHUD.asi
DualWieldParryingScriptDragon.asi
skse_1_8_151.dll
ScriptDragon.dll
flowchartx32.dll
dinput8.dll
d3d9.dll
binkw32.dll
atimgpud.dll
steam_api.dll
ssce5432.dll
skse_steam_loader.dll