After looking at this in IE, my impression is that it has nothing to do with clear:both. Simply, there is an error/browser quirk in IE6 that causes your main column to expand in width, which forces the side column down below. (You’ll notice that the two columns work fine on other pages in IE6.)
I’m guessing it’s something to do with the way you have your article previews on your home page coded — perhaps dealing with the fact that you set a width and also padding/margin on your #post-info div. I’ve found that making sure that you don’t set a width and padding/margin on the same element tends to help with browser compatibility issues.
If I find something specific that will help, I’ll let you know.
— Not related, but you realize that you can only use an id once on a page? For example, on your home page, you repeat the #post-info id several times.
In regards to your question about ids… Ids are intended to be unique elements, and can only be used once per HTML page — that’s just the way they work. Classes can be used on multiple elements on the same page.