If you examine the HTML in Developer mode, you’ll see that the publishing order of the “MainContent” HTML Extension objects is incorrect. It appears before the navigation buttons, even though the buttons are between the SkipTheMainContent HTML object and the MainContent HTML object in your title. The only two objects between look like the groups you have for Resources and Glossary, which are both set to “Always on Top”, which explains why.
I believe this is a bug in v18 with how the HTML Extension object (when used as a Custom Div) is written out. It does not adhere to the order in the Title Manager, but instead is written first, as if it is set to “Always on Top”. If you put an HTML Ext Custom Div at the page-level, it will be written with title-level objects.
As a work-around, you could switch MainContent to a text object, and then change your SkipTheMainContent href to point to that object by name (e.g. text612925anc).
So instead of: a class=”ms-skip” href=”#mainContent” SKIP TO MAIN CONTENT /a
Use: a class=”ms-skip” href=”#text612925anc” SKIP TO MAIN CONTENT /a
(sorry, had to remove HTML tags so that the hyperlink can be viewed)