Its showing up different because of the code in the responsive section. The responsive section of the css adjusts the menu to be vertical….but again, Wes is redesigning this to be horizontal instead. Here is an example – http://demo.appfinite.com/epik/ view in a mobile browser, or resize your browser to see the difference.
The only thing I can recommend is to copy the menu/nav code from the 2nd responsive section –
@media only screen and (min-width: 600px) and (max-width: 960px)
and add those same adjustments to the top/first responsive section under this –
@media only screen and (max-width: 600px)
It will take some effort, but it can be done….and it will probably be easy if you’re good with css. Other than that, there will be an entirely new version of this theme when Genesis 2.0 comes out (which will be soon).