I'm thinking that perhaps Barnabas could have been in the course of making Quentin into a Leviathan follower when he was interrupted, and that the interruption inflicted damage to Quentin's mind, causing the amnesia.
I like that one. See, with a little thought, all these awkwardnesses could have been improved. I never saw Barnabas as being under total control, though... I guess I thought of it as powerful hypnotic suggestion, where the subject is not supposed to be capable of acts he finds especially abhorrent (on a personal level in this case). As for Josette, I thought of that as a subconscious threat that was there as a backup in case the primary control of Barnabas failed.
How about when we find out the Book says never to kill people?! Let's make a list:
The Book says we play nice
[spoiler]Q not killed in hospital
Blair turns up
Peter Bradford and his wild story... I'm not convinced that Ned Stuart didn't get drunk and put a noose around his neck and make up the whole thing.
Jeb finds true love and gets nice
Josette/Kitty a prisoner[/spoiler]