The answer I got was what I expected, but I wanted to make sure I gave correct information:
There's an "!important" override that is preventing the theme options from applying. To fix it, all that needs to be done is removing the "!important" from the CSS:
template.css line 305 -
#s5_menu_wrap.s5_wrap, #s5_menu_wrap.s5_wrap_fmfullwidth {
border-bottom: 1px solid #e7e6e6;
height: 61px !important;
width: 100%;
}
That should give you the results you need.