I have little hope finding any help since it looks like an iBooks bug to me, but here's what I found:
If I have in my EPUB file an XHTML document containing only a
<video> element with the
autoplay="autoplay" attribute, it starts playing when I land on the page, and pauses when I go to the next or previous page, just as expected.
Now if my document contains anything else, like a
<div> or even the letter
F or whatever, before or after the
<video> element, the video doesn't play automatically.
Not sure if I should post an answer explaining that, because my problem is not solved, but this question might help others having the same kind of issue and not needing to include else on the page.