I'm able to reproduce the same issue you are having (I'm assuming you are talking about how the menu looks on the content page).
The problem seems to be that the menu is too big to fit in the top navigation area of the template. You could see on the home page you don't have that problem, but it only happens on the content pages because the home link is added to the menu.
A work around would be to remove one of the links on the content page by deleting it in step 3 of the wizard.
Another way you could do those would be to adjust the width of the outerWrapper, but i think that is going to require more work, because the background images will have to be adjusted as well.
If you are still having the issue, please provide me with a link so i can debug the issue further.