There is currently a bug in WoW 10.1.5 that completely clears your Objective Tracker when you log in. See for example this forum thread.
So it's not AQT that no longer remembers your manually tracked quests. (AQT repopulates the cleared tracker with the current zone quests, but cannot add your manually tracked quests, because the "manually added" flag gets cleared by the WoW bug too.)
Note that AQT's base functionality is not affected by the WoW bug, it's just that your manually added quests will not be persistent in the tracker until Blizz fixes it.
There is currently a bug in WoW 10.1.5 that completely clears your Objective Tracker when you log in. See for example this forum thread.
So it's not AQT that no longer remembers your manually tracked quests. (AQT repopulates the cleared tracker with the current zone quests, but cannot add your manually tracked quests, because the "manually added" flag gets cleared by the WoW bug too.)
Note that AQT's base functionality is not affected by the WoW bug, it's just that your manually added quests will not be persistent in the tracker until Blizz fixes it.