During a key if you exit the instance and re-enter the timer gets set back to 0.

Hm, the timer should try to sync with teammates who have similar addons, and fall back to the blizzard timer if it fails to do that. I'll check if there's any issue with that. Did you do anything specific, or just exit and re-enter? Did you log out in between?

Have not been able to reproduce this since the issue was opened. If the bug occurs again, please open another issue with information attached.