tax_query not working, anything change in latest version?

I’m using the following code to do a tax_query and it doesn’t seem to work anymore..

At some point it was working and for the life of me it wont, anymore.

<?php

	global $pf_override;

	class PF_override {

		public $site_terms = array();

		function __construct() {

			// add filters
			add_filter( 'init', array( &$this, 'populates_site_terms' ) );
			add_filter( 'pre_get_posts', array( &$this, 'filter_query' ) );
		}

		function populates_site_terms() {

			// my actual function does some processing and
			// checks caches and combines IDs from multiple
			// different sources here and then sets site_terms 

			$this->site_terms = array( 1, 2, 3 );
		}

		function filter_query( $query ) {

			// not the main query?
			if ( !$query->is_main_query() ) {
				return $query;
			}

			// have terms to filter by?
			if ( !empty( $this->site_terms ) ) {

				// construct tax_query
				$tax_query = array(
					'taxonomy' 	=> 'site_category',
					'field' 	=> 'id',
					'terms' 	=> $this->site_terms,
					'operator' 	=> 'IN'
					);

				// this needs to be an array of arrays
				$taxquery = array(
					$tax_query
				);

				// set this..
				$query->set( 'tax_query', $taxquery );
			}

			// return new query object
			return $query;
		}
	}

	// not the admin? init class
	if ( !is_admin() ) {
		$pf_override = new PF_override();
	}

?>

Taxonomy is added like so:

function PF_register_post_type() {
		$labels = array(
			'name'              => _x( 'Site Category', 'taxonomy general name' ),
			'singular_name'     => _x( 'Site Category', 'taxonomy singular name' ),
			'search_items'      => __( 'Search Site Categories' ),
			'all_items'         => __( 'All Site Categories' ),
			'parent_item'       => __( 'Parent Site Category' ),
			'parent_item_colon' => __( 'Parent Site Category:' ),
			'edit_item'         => __( 'Edit Site Category' ),
			'update_item'       => __( 'Update Site Category' ),
			'add_new_item'      => __( 'Add New Site Category' ),
			'new_item_name'     => __( 'New Site Category Name' ),
			'menu_name'         => __( 'Site Category' ),
		);

		$args = array(
			'hierarchical'      => true,
			'labels'            => $labels,
			'show_ui'           => true,
			'show_admin_column' => true,
			'query_var'         => true,
			'rewrite'           => array( 'slug' => 'sitecat' ),
		);

		register_taxonomy( 'site_category', array( 'post', 'page', 'attachment', 'revision', 'nav_menu_item' ), $args );
}

add_action( 'init', 'PF_register_post_types', 1 );

In my footer.php I add this code:

$GLOBALS['wp_query']->request

I get this as a result when going to mydomain.com/testing:

SELECT wp_posts.* FROM wp_posts  WHERE 1=1  AND wp_posts.post_name = 'testing' AND wp_posts.post_type = 'post' ORDER BY wp_posts.post_date DESC

The $pf_override variable shows $pf_override->site_terms to be set as an array of

array( [0] => 1, [1] => 2, [2] => 3 )