My site now appears to have two navigation menus at the top of the page
Most likely you used to have a menu and a 'breadcrumb' view and did not update the custom theme to conform with the changes in v2.0.9+. You'll need to edit your theme template (index.php and subthemes) a replace the part which shows:
...'view'=>'Breadcrumb'...
with
...'action'=>'breadcrumb','view'=>'breadcrumb'
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