Custom Taxonomy Template won't show any menus

Question

This is how I can start describing this, it's a very strange error that maybe something else but this is the first symptom I have.
I have a custom template[taxonomy-location_types.php] that shows, a custom post type [locations] by it's custom taxonomy[location-types].

If you visit the home page you will see a menu editorial, travel, etc.
Now if you look here on this taxonomy page
The menu is gone, there are other queries that aren't firing but I'm focussing on this as a primary issue.

I have generated output from nav-menu-template.php like so:

    if ( $menu && !is_wp_error($menu) && !isset($menu_items) )
{
    write_log($menu);
    $menu_items = wp_get_nav_menu_items( $menu->term_id, array( 'update_post_term_cache' => false ) );
    write_log($menu_items);
}

and I get this:

[31-Aug-2017 15:27:52 UTC] WP_Term Object
(
    [term_id] => 2
    [name] => Header Menu
    [slug] => header-menu
    [term_group] => 0
    [term_taxonomy_id] => 2
    [taxonomy] => nav_menu
    [description] => 
    [parent] => 0
    [count] => 6
    [filter] => raw
)

[31-Aug-2017 15:27:52 UTC] Array
(
)

[31-Aug-2017 15:27:52 UTC] WP_Term Object
(
    [term_id] => 3
    [name] => Footer One
    [slug] => footer-one
    [term_group] => 0
    [term_taxonomy_id] => 3
    [taxonomy] => nav_menu
    [description] => 
    [parent] => 0
    [count] => 5
    [filter] => raw
)

[31-Aug-2017 15:27:52 UTC] Array
(
)

So it sees the menu but for some reason return no items in either menu.
I have turned off all plugins and still get the same result, I have also eliminated all other queries on this page to see if there was conflict and this still this happens.

Any insight on this one would be great not sure where to look next for issues.

Answer 1

Chalk another one up for RTFM, I had a pre_get_posts hook altering the query and I didn't ensure that the query it was altering was just the $query->is_main_query() because strangely enough this alteration was getting into the nav_menu query.

query monitor is now my new best friend.