One thing I see that need corrected, but is not causing the misalignment of the boxes is that in #wrapper in your CSS, add a width declaration at 1000px, which is the width of your header. Right now stuff is hanging outside of the right side of the wrapper which is not a good thing.
I'm afraid I'm at a little bit of a loss as to what is causing it, and unlike you, refreshing the page is not causing things to align properly for me. It stays misaligned.
I'll tag this to have it moved to the CSS forum since this is likely a CSS related issue and hopefully @designsimply will see it and look into it for you.