I'm not able to figure out what configuration in ZQuest causes this because I ran into it playing Saffith's Antiquity.
http://www.zeldaclassic.com/viewquest.php?q=402
Simply put, entering Ganon's room causes Link to lock up. He gets stuck perpetually holding the Triforce over his head with Ganon never appearing. A Ganon room in a test quest I made worked fine though, and unfortunately Saffith passworded his quest (I may be the only one who has always taken the view that passwording quests is silly). In any case, this renders the quest unbeatable, and I have no way of knowing if this is a ZC bug or just a problem with the quest itself. Sorry if it is a problem with the quest itself, but I think I'm safe in presuming that it has been beatable in other builds.