This may sound condescending (which I do NOT intend), but are you exiting Skyrim between tests? If you change something in the CK while the game is still running, you get crazy behavior like that.
Aside from that, I don't really know what else it could be. Maybe you have some scripting, a location, or aliases that haven't been filled/assigned/whatever? This may be the case if you entered the game normally, THEN coc to you area... it should work as expected. But if you try coc from the Title Screen, there are loads of properties and aliases/etc that aren't properly intitialized in Vanilla. Either they may be causing your issue or a similar effect in your mod's data; like if your coc marker is somehow linked to an alias or something session-sensitive.
ONE other suggestion would be to double-check the Skyrim Launcher to see what ESPs are enabled. If you practice version control (rename your ESPs after changing things), any NEW ESPs the game finds in your Data/ folder are AUTOMATICALLY enabled. If you have more than one version of the same mod running simultaneously, it gives you CRAZY behavior... which may be your problem.
[For instance, I have a Player home that has a custom sound assigned to a night stand when opened... if 2 versions of the mod are enabled, THAT sound plays as soon as you load ANY game - no matter where in the game you load to! Why THAT sound, why when loading a saveGame (or starting a new one.. even coc), and why sometimes when opening other random doors? Nooooo idea... just illustrates how strange things can get for seemingly no reason. It's a funny reminder for me to disable the older version of the ESP... though your reminder, if that's what it is, is less than hysterical.]