Index: wp-includes/query.php
===================================================================
--- wp-includes/query.php	(revision 17545)
+++ wp-includes/query.php	(working copy)
@@ -1240,6 +1240,15 @@
 	var $query_vars_hash = false;
 
 	/**
+	 * Whether query vars have changed since the initial parse_query() call.  Used to catch modifications to query vars made
+	 * via pre_get_posts hooks.
+	 *
+	 * @since 3.1.1
+	 * @access private
+	 */
+	var $query_vars_changed = true;
+
+	/**
 	 * Resets query flags to false.
 	 *
 	 * The query flags are what page info WordPress was able to figure out.
@@ -1395,6 +1404,7 @@
 
 		$this->query_vars = $this->fill_query_vars($this->query_vars);
 		$qv = &$this->query_vars;
+		$this->query_vars_changed = true;
 
 		if ( ! empty($qv['robots']) )
 			$this->is_robots = true;
@@ -1628,6 +1638,8 @@
 			$this->set_404();
 
 		do_action_ref_array('parse_query', array(&$this));
+
+		$this->query_vars_hash = md5( serialize( $this->query_vars ) );
 	}
 
 	/*
@@ -1685,7 +1697,7 @@
 		}
 
 		// Category stuff
-		if ( !empty($q['cat']) && '0' != $q['cat'] && !$this->is_singular && md5(serialize( $this->query_vars ) ) != $this->query_vars_hash ) {
+		if ( !empty($q['cat']) && '0' != $q['cat'] && !$this->is_singular && $this->query_vars_changed ) {
 			$q['cat'] = ''.urldecode($q['cat']).'';
 			$q['cat'] = addslashes_gpc($q['cat']);
 			$cat_array = preg_split('/[,\s]+/', $q['cat']);
@@ -1739,7 +1751,7 @@
 		}
 
 		// Tag stuff
-		if ( '' != $q['tag'] && !$this->is_singular && md5(serialize( $this->query_vars ) ) != $this->query_vars_hash ) {
+		if ( '' != $q['tag'] && !$this->is_singular && $this->query_vars_changed ) {
 			if ( strpos($q['tag'], ',') !== false ) {
 				$tags = preg_split('/[,\s]+/', $q['tag']);
 				foreach ( (array) $tags as $tag ) {
@@ -1811,8 +1823,6 @@
 			);
 		}
 
-		$this->query_vars_hash = md5(serialize( $this->query_vars ) );
-
 		$this->tax_query = new WP_Tax_Query( $tax_query );
 	}
 
@@ -1884,6 +1894,15 @@
 
 		$q = $this->fill_query_vars($q);
 
+		// Set a flag if a pre_get_posts hook change the query vars.
+		$hash = md5( serialize( $this->query_vars ) );
+		$this->query_vars_changed = false;
+		if ( $hash != $this->query_vars_hash ) {
+			$this->query_vars_changed = true;
+			$this->query_vars_hash = $hash;
+		}
+		unset($hash);
+
 		// First let's clear some variables
 		$distinct = '';
 		$whichauthor = '';
@@ -2444,6 +2463,15 @@
 			$where .= ')';
 		}
 
+		if ( $this->query_vars_changed ) {
+			$meta_query_hash = md5( serialize( $q['meta_query'] ) );
+			$_meta_query = $q['meta_query'];
+			unset( $q['meta_query'] );
+			_parse_meta_query( $q );
+			if ( md5( serialize( $q['meta_query'] ) ) != $meta_query_hash && is_array( $_meta_query ) )
+				$q['meta_query'] = array_merge( $_meta_query, $q['meta_query'] );
+		}
+
 		if ( !empty( $q['meta_query'] ) ) {
 			$clauses = call_user_func_array( '_get_meta_sql', array( $q['meta_query'], 'post', $wpdb->posts, 'ID', &$this) );
 			$join .= $clauses['join'];