To my knowledge, none of those quests have been altered. In order to check for existing bugs in those situations, I would need save files made during the problems, as they arise, sent to me, where I can try to troubleshoot. If you have gone well past the problem, I don't think I will be able to troubleshoot. There may have been specific circumstances that led to the error that I am not able to replicate, because in the few playthrough's of those quests made so far, I have not encountered these particular problems yet.