A long time ago, when I first started playing, like almost 2 years ago it would seem, I had the same problem. It seemed like every clear quest would never end. I think my game was messed up and I had to do that verify files thing to fix it. Even after it was working again I avoided clear quests for a long time because I didn't want to waste my time in them in case they wouldn't finish.
I do them all the time now, and I can't remember one not working since the verify files thing. Now, I forget my courier satchel all the time and get a failed quest as I'm motoring back to the trader to get my reward.
In my opinion, both quests still suffer from a very, very broken design. Clear quests should be a certain number of zombies, about 10% less than the total number of zombies. Fetch quests (really all quests) should warn you when you leave the zone and give you a certain number of seconds, say 10, to get back in the zone before you fail.
Now that I'm thinking about it, I might have reinstalled to fix the clear thing, but I would certainly recommend starting with the verify files thing first.