Where are the two grey bars between the header and the rest of the page created?
I can't get the grey bars to line up with the menu
If you are using the 'ata-adsense.txt' starter settings, it is setup with a background image that has two gray lines spanning the page. These lines originally line up with the menu's. By making changes to the header (image height, font sizes) you can change the menu bar's locations so they don't line up.
Either change the background image (ATO->Body, Text & Links->Body Style) or change your heading settings so it lines up.