Of course I spoke too soon. The formatting was fixed but I just noticed the menus are all wrong on the category pages with themes assigned. It is not using the menus selected in wordpress for any pages set to use any theme other than the default.
As an example, now that I switched to a different theme it added all of the page links in the footer and changed the primary nav menu to display categories instead of the menu that I created.
If I switch back and forth between the templates the menus are configured correctly. The issue only occurs on categories where I have assigned a non-default theme.