The problem is that the Facebook Comments box renders with a transparent background. That is good for taking on the look of the current page. However, we're using pre tags in the area that is getting overlapped, and content in those tags is preformatted and can't be altered dynamically. If you'll notice though, the Subscription buttons (using normal Divs) do get reorganized around the comment box as it grows. That's the proper behavior.
We'll have to change how we're using the preformatted tags to accommodate this issue. There's no z-index or other CSS setting that can get around it on our site, at least. If you want us to look at your site, I can let you know what may need to change with your configuration.
Thanks,
Alex