Okay, so it looks like I was a bit premature. The problems the new test version has with AO3 and html are not over. Take a look at the story I attached. The link is this (sorry, it's a long one this time):
http://archiveofourown.org/works/62539 (The Water Grinds the Stone)
It made right-aligned text left-aligned, and somehow put <big> tags in there that made random words huge. (Looks like the problem is that the source text has the font tag "big".) It's unreadable.
To be clear, I don't see the same problem with its epub version. In that one it simply makes right-aligned text left-aligned.
Another example is this one:
http://archiveofourown.org/works/152837 (The Weight of Water)
In this one, there are no huge words, but the text style in the body is messed up, in both html and epub.
In case it helps, I've attached my personal.ini too.