Perhaps I should explain it better, since it seems like you might not get it.
The bot "can" run while there is a popup. It will defend itself.
While there is a UserDialog, the "popup", the bot will do nothing except defend itself.
This means that when there is a popup, it will not complete quests, or pull mobs.
This dialog typically closes after 30 seconds.
You are botting, so you are losing a negligible amount of time.
Unless you are talking about the profile stopping itself because your character cannot complete the quest, which throws a UserDialog telling you why it is stopped instead you leaving you to guess.
However, in each thread you have made complaining about it, you are not clear on what type of popup you have a problem with.