I was also surprised about how out of touch Mr. Hat-and-Cloak seemed to be. Where is he getting his information? He seems to have an absolutely abysmal model of both how Harry thinks and how Hermione thinks Harry thinks. He hasn't been much better in previous cases. It wouldn't have taken much snooping around to get better informed than he seems to be.
I'm fairly confident that Mr. Hat-and-Cloak is well-informed but aiming to miss-inform. Why he wants to make Hermione suspicious of Harry, I'm not sure.
Update: Discussion has moved on to a new thread.
The hiatus is over with today's publication of chapter 73, and the previous thread is approaching the 500-comment threshold, so let's start a new Harry Potter and the Methods of Rationality discussion thread. This is the place to discuss Eliezer Yudkowsky's Harry Potter fanfic and anything related to it.
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six, seven. The fanfiction.net author page is the central location for information about updates and links to HPMOR-related goodies, and AdeleneDawner has kept an archive of Author's Notes.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: