A few weeks ago, it was discovered that JAWS 10 and 11 (and so far, JAWS 12 beta), when used in conjunction with Firefox 3.6 (or Firefox 4 beta), simply cannot find or use any content contained within the HTML5 header element. Terrill Thompson's test page makes this clear. It turns out that it is a bug with Freedom Scientific's screen reader. Whether or not it will be fixed for the final release of JAWS 12, or a patch for JAWS 10 or 11 provided, remains to be seen.
In any case, without knowing what the future holds, or exactly what combination of JAWS and Firefox a user might have, I've been compelled to go through this site and remove all instances of the header element. Honestly, and quite sadly, with the problems some popular Windows-based screen readers have with basic HTML5 elements, especially when combined with WAI-ARIA attributes (see HTML5, ARIA Roles and Screen Readers in May 2010), I'm really starting to reconsider my decision to use HTML5 at all at this point.
Update (Oct. 13, 2010): See the post Header is Back!.
HeaderElements Removed