Well, there's really no need to "clear them out". Please see
This Post to see another way to do this. (and, yeah, I posted the original but I just didn't feel like typing it all again
)
Your test jogged my memory. There used to be a problem with the same thing some time ago (like at the beginning of Cataclysm live release), and I think the only solution was to disable the automatic quest stuff. However, I don't think Carbonite is the only addon that caused the problem. I remember seeing posts about it on the Blizzard WoW forums at the time, and the solution was disabling the automatic quest pick up and turn in.
However, since you're having trouble with only the turn ins, why not just disable that option and see if the problem continues.