One place where I see this fix things is in the blog sidebar where the sidebox heading text is clickable and the link is /index.php?main_page=wordpress

If you leave the wp sideboxes in the default position, they work well, but I think if you try moving them to the right column a few things break that need a few tweeks to the WP default template. I've had to fix that before and I think it had to do with commenting out calling the proper wp side column. (comment it out I think.