I seem to be having this exact same problem. I didn’t change anything, except one day last week it just stopped displaying the sidebar properly on the root page of the blog (http://www.modernaugury.com/jumbledmusings/). The problem persists no matter what theme I choose or what browser I use to view it. So it would appear to be a non-theme, non-browser issue.
I seem to have fixed it…? I clicked on the option under “Writing” settings for WordPress to automatically correct invalidly nested XHTML. I’m not sure if that really did the trick, or if it was just a coincidence though. I made a couple of changes at the same time, but that’s the only one that I can imagine would be meaningful.
it happen to me before, but after i trouble shoot i found that it because of my last post, wrong HTML nested. I think your problem due to this.
It happens same to me.
After I changed the theme, the sidebar appears at the bottom and whatever themes I change.
The only thing I can do is to change the theme back……