I think that with the popularity of the fic, most people are making their way to it with recommendations that it is already good, so they will have a different reading strategy than somebody browsing for something worth reading.

I noticed quite a while ago with considerable disappointment that you had changed

Harry looked up at the sky, and began laughing. He couldn’t seem to help himself. This is the most improbable day of my life.

to

There was a long silence in the backyard. Then a boy's voice said, calmly and quietly, "What."

(with annoyance at the inappropriate punctuation on top of it: if you must avoid a question mark here, use an ellipsis, not a period!)

...but until seeing Eneasz's comment I totally failed to notice that you had deleted that whole paragraph! Shame!

As a regular reader of neither SF nor fanfiction, I don't really care about the "expectations" of those genres. As far as I'm concerned, Methods of Rationality is its own genre, and that paragraph was very much stylistically consistent with the rest of the story, funny parts and all, and it was particularly consistent with Harry as we have come to know him.

Actually, this part (minus the phrase "unmotivated conspiracies") sounds like something out of British children's fiction:

Even if Harry tried to explain the day’s events by sudden insanity or unmotivated conspiracies, that didn’t put everything back to normal. It didn’t make the day’s events expected. It didn’t make him feel not-confused. There was no denying that something very, very, very odd was going on

Anyway, maybe the passage could be tweaked for lightheartedness if that's what you prefer, but I was really sorry to see the point about noticing confusion disappear.