Thanks so much for looking at this Pioneer, I didn't know you have, I got no notice.
I'm not using a custom page template so that's why it's so confusing. It's a child theme of twenty twelve so it uses that default. The pages that I have created are coming out wrong but the category ones are right, and I don't see how the index.php and the category.php are causing a difference. I'm still new, if I have some links that are in one format and some in another does that mess it up? This is my first site that isn't pages, strangely enough, and i"m working with blog posts.
I have these two types:
The closing div above the main one when I look at it with the Firefox bug.
I have been over this code like crazy. It's just a simple child theme, but I am having to learn about creating links for category pages and feeling a little shaky. :)