Yesterday I did the quest "Tomb of the Blighted". After finishing the quest I still had the blighted effect. It was permanent: I could use a Heal scroll every few seconds to cure my ability score damage; but each blight countdown would apply them again. This persisted through re-logging my character.
The only solution was to ask the quest-giver to repeat the quest and have the purifying water fountain cure my blight, and then recall. This meant that I was no longer flagged for The Cursed Crypt.
I think the best bug fix would be to make it so that leaving the quest removes the blighted effect. And maybe as a backup bug fix, make re-logging in town remove all negative effects on your character.