Return to top anchor on index page doesn’t go to top (Header)

I have modified a theme for my new blog and I have incorporated a “Back to Top” link at the bottom of the page (index page) by placing the following code on the top of my page –
When this is placed as the second line of code, after – <?php get_header(); ?> The page doesn’t go all the way to the top (header) where my nav is. It does go all the way to the top if I put it in my first line of code, however, I just noticed that when in the first line the page is messed up in IE. I don’t understand why this doesn’t work with IE. Is there a way around this?
thanks