I have only 1 menu enabled and it is at the top of the list but the breadcrumb is still pulling from the main menu.
Line 326 is appending the menu to the list, unfortunately it is adding it to the end of the list that is passed to menu_set_active_menu_names;
I corrected it by changing "$active_menus = $menu_name;" to "array_unshift($active_menus, $menu_name);"
I can create a patch for this, I just didn't know if this is happening because of some weird config on my end or if it is actually a bug. It would seem like it wouldn't be working for anyone (unless they use the regex piece).