Navigation bar not showing like in html

[eatons]

The problem is markup code inside the 'admin/inc/theme_functions.php'

I don't know if you found your answer to the problem, but I did, and I wrote it in a tutorial covering that and other aspects of working with GetSimple themes. Here is a link to the actual solution within the tutorial, and from there you'll see a link for which you can download the solution.
http://eatons.net/tutorials/innnovationoutline/addendum