The only constants I’ve been able to put my finger on so far are that it only happens on the home page (never on individual post pages) and when using Firefox 3.
I’m working with an HTML validation tool right now and will be fiddling with things for the rest of the afternoon. If you’ve seen the sidebar behaving badly and a quick refresh doesn’t whip it back into shape, could you please share in the comments 1) which browser you’re using, 2) what page you’re viewing (home page or something else), and 3) whether the sidebar is missing completely or if it’s appearing below all the posts at the bottom of the page? Thank you!