Menu Disappears on Category Pages

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I know this is an old question but seems that is still unresolved. As @Milo said you may have an incorrect pre_get_posts implementation.

Most people do this like this (example):

add_filter( 'pre_get_posts', 'query_post_type' );

function query_post_type( $query ) {
    if ( is_category() ) {
        $post_type = get_query_var( 'post_type' );
        if ( $post_type ) {
            $post_type = $post_type;
        } else {
            $post_type = array( 'nav_menu_item', 'post', 'departments' );
        }
        $query->set( 'post_type', $post_type );

        return $query;
    }
}

But we must change the line: $post_type = $post_type; and pass 'nav_menu_item' to the $post_type in order to menu to display, as follow:

add_filter( 'pre_get_posts', 'query_post_type' );
function query_post_type( $query ) {
    if ( is_category() ) {
        $post_type = get_query_var( 'post_type' );
        if ( $post_type ) {
            $post_type = array( 'nav_menu_item', $post_type );
        } else {
            $post_type = array( 'nav_menu_item', 'post', 'departments' );
        }
        $query->set( 'post_type', $post_type );

        return $query;
    }
}

I hope this help people who do this wrong and sorry for my bad English.

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