Well then, sorry about that. Sounds like quest continuity is a recurring problem so I'll have to organize things a bit. It might help if I just make the quest tracker editable to playtesters so you can un-bug the game if you get stuck (or skip segments you've already seen, because that will get annoying eventually). Will push an update later this week.
Actually, I have that same issue with the SCP driver for my DS3. Windows thinks I have a joystick plugged in at all times. Probably makes more sense to check which input method was last used and treat that as the default.