I'm probably going to look into it later, but while using jQuery today on a html5 <section> node which I had applied position: absolute; to fadeIn/fadeOut was acting really screwy on it.
fadeOut didn't seam to work, and fadeIn did something weird with opacity on things that were already displayed.

For a test I think you should be able to reproduce the issue by putting a <section> in the page and giving it a position: absolute; style and trying to use fadeIn/Out on it.

I found this issue in both Firefox and Chromium, haven't tested other browsers yet but it looks like a jQuery bug.