I'm running 3.0.1 and have noticed this code right after the opening body tag:
It's also repeated again right before the close of the body tag.
See my site here:
On another site (same server) this is injected into the code before the closing body tag:
I found some base64 stuff in each theme's index.php, but the code remains. I deactivated all my plugins and then reinstalled WordPress. It's still there. I've obviously missed something.
I'm guessing it's tied into get_header() and get_footer() somehow. Could someone point my in the direction of the files I should be looking for. This was the best I could fine online.