I think I figured it out.
In menus are 3 lists. Most Recent, View All and Search
for unknown reasons Customizr was only looking at the Most Recent list and not the View All ( I also blame WP as the Most Recent did not actually include the Most Recent) when I customized the menu to match the new Appearance style the menus did not actually read the correct location. They were reading God knows where since the location was never actually used by the pages.
Anyway thanks for looking.
