Might be the theme but there is also a conflict with this great addon. If you try to add in something on a tab that already exists in the menu, the subnav will only show for the addon. For example, create a link to a subcategory of the resource manager like "themes." Normally you'll have the submenu show for add a resource, etc. But all you'll get is the name of the tab in the submenu. On my custom theme I get both, but with the name of the submenu in the addon on on top of the first entry in the subnav for the other addon like RM. So I'll either see "themes" in the subnav or the name "themes" will be laid on top of the existing subnav (add a resource) in the subnav.
This is an amazing addon. I just cannot figure out a way to hide XF nav items properly and replace them with this addon.