If you're on a PvP server in World of Warcraft, refrain from activating the Cloak of Shadows during a run on any PvP objective. Why? Because when you deactivate the cloak, it removes the flag from your inventory. This can be particularly nasty if you're almost at the end of the run since you'll have to redo the entire instance.
The above mentioned bug was reported by a poster named Rhoderic on the WoW Europe Forums and Blizzard Localization QA Tootamia gave word that they're going to look into the problem. So far, there's been no word whether or not it has been fixed.
Knowing Blizzard, the fix could come anytime between one day to as long as a couple of months. Rogues will probably be want to wait until Blizzard has fixed this bug before making any more runs. Once again, don't activate the Cloak of Shadows when doing a PvP objective on a run.
Unless you're absolutely sure they've fixed the bug. You'll probably end up getting very frustrated if you do.