Primary Links appear even when disabled in theme config.

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Change "SOURCE FOR THE PRIMARY LINKS:" to "No primary links"

The Primary Links should no longer display.

If you want to remove the gray bar, do this:

In style.css, change min-height to zero in this div.

#navigation {
width: 100%;
clear: both;
min-height: 0em;
border-bottom: 1px solid;
}

In css/ie-7.css, remove or comment out display: inline-block; from this div.

#navigation .wrap-center {
/* display: inline-block; */
}

In css/ie-6.css, remove or comment out display: inline-block; from this div.

#navigation .wrap-center {
/* display: inline-block; */
}

Sorry, this was my fault. Wasn't exactly expecting anyone not to use the primary links.

I just corrected this issue, by respecting the chosen setting and not displaying any markup if the primary links box has not been checked. As a result I also had to set a default height of 100px for the header. This number can be changed on the theme settings page.

The change has been committed.