Index: wp-includes/default-filters.php
===================================================================
--- wp-includes/default-filters.php	(revision 18927)
+++ wp-includes/default-filters.php	(working copy)
@@ -254,6 +254,7 @@
 add_action( 'publish_post',               '_publish_post_hook',                       5, 1 );
 add_action( 'save_post',                  '_save_post_hook',                          5, 2 );
 add_action( 'transition_post_status',     '_transition_post_status',                  5, 3 );
+add_action( 'transition_post_status',     '_update_term_count_on_transition_post_status', 10, 3 );
 add_action( 'comment_form',               'wp_comment_form_unfiltered_html_nonce'          );
 add_action( 'wp_scheduled_delete',        'wp_scheduled_delete'                            );
 add_action( 'admin_init',                 'send_frame_options_header',               10, 0 );
Index: wp-includes/taxonomy.php
===================================================================
--- wp-includes/taxonomy.php	(revision 18927)
+++ wp-includes/taxonomy.php	(working copy)
@@ -2447,13 +2447,7 @@
 		call_user_func($taxonomy->update_count_callback, $terms, $taxonomy);
 	} else {
 		// Default count updater
-		foreach ( (array) $terms as $term) {
-			$count = $wpdb->get_var( $wpdb->prepare( "SELECT COUNT(*) FROM $wpdb->term_relationships WHERE term_taxonomy_id = %d", $term) );
-			do_action( 'edit_term_taxonomy', $term, $taxonomy );
-			$wpdb->update( $wpdb->term_taxonomy, compact( 'count' ), array( 'term_taxonomy_id' => $term ) );
-			do_action( 'edited_term_taxonomy', $term, $taxonomy );
-		}
-
+		_update_post_term_count( $terms, $taxonomy );
 	}
 
 	clean_term_cache($terms, '', false);
@@ -2846,10 +2840,21 @@
 	global $wpdb;
 
 	$object_types = is_array($taxonomy->object_type) ? $taxonomy->object_type : array($taxonomy->object_type);
+	
+	foreach ( $object_types as &$object_type )
+		$object_type = reset( explode( ':', $object_type ) );
+	
+	$object_types = array_unique( $object_types );
 	$object_types = esc_sql($object_types);
 
 	foreach ( (array) $terms as $term ) {
-		$count = $wpdb->get_var( $wpdb->prepare( "SELECT COUNT(*) FROM $wpdb->term_relationships, $wpdb->posts WHERE $wpdb->posts.ID = $wpdb->term_relationships.object_id AND post_status = 'publish' AND post_type IN ('" . implode("', '", $object_types) . "') AND term_taxonomy_id = %d", $term ) );
+		
+		// Attachments can be 'inherit' status, we need to base count off the parent's staus if so
+		if ( in_array( 'attachment', $object_types ) )
+			$count = $wpdb->get_var( $wpdb->prepare( "SELECT COUNT(*) FROM $wpdb->term_relationships, $wpdb->posts p1 WHERE p1.ID = $wpdb->term_relationships.object_id AND ( post_status = 'publish' OR ( post_status = 'inherit' AND post_parent > 0 AND ( SELECT post_status FROM $wpdb->posts WHERE ID = p1.post_parent ) = 'publish' ) ) AND post_type IN ('" . implode("', '", $object_types) . "') AND term_taxonomy_id = %d", $term ) );
+		else
+			$count = $wpdb->get_var( $wpdb->prepare( "SELECT COUNT(*) FROM $wpdb->term_relationships, $wpdb->posts WHERE $wpdb->posts.ID = $wpdb->term_relationships.object_id AND post_status = 'publish' AND post_type IN ('" . implode("', '", $object_types) . "') AND term_taxonomy_id = %d", $term ) );
+		
 		do_action( 'edit_term_taxonomy', $term, $taxonomy );
 		$wpdb->update( $wpdb->term_taxonomy, compact( 'count' ), array( 'term_taxonomy_id' => $term ) );
 		do_action( 'edited_term_taxonomy', $term, $taxonomy );
Index: wp-includes/post.php
===================================================================
--- wp-includes/post.php	(revision 18927)
+++ wp-includes/post.php	(working copy)
@@ -2731,12 +2731,6 @@
 	$post->post_status = 'publish';
 	wp_transition_post_status('publish', $old_status, $post);
 
-	// Update counts for the post's terms.
-	foreach ( (array) get_object_taxonomies('post') as $taxonomy ) {
-		$tt_ids = wp_get_object_terms($post_id, $taxonomy, array('fields' => 'tt_ids'));
-		wp_update_term_count($tt_ids, $taxonomy);
-	}
-
 	do_action('edit_post', $post_id, $post);
 	do_action('save_post', $post_id, $post);
 	do_action('wp_insert_post', $post_id, $post);
@@ -5312,4 +5306,20 @@
 }
 add_filter( 'wp_get_object_terms', '_post_format_wp_get_object_terms' );
 
+/**
+ * Update the custom taxonomies' term counts when a post's status is changed. For example, default posts term counts (for custom taxonomies) don't include private / draft posts.
+ * 
+ * @access private
+ * @param string $new_status
+ * @param string $old_status
+ * @param object $post
+ * @since 3.3.0
+ */
+function _update_term_count_on_transition_post_status( $new_status, $old_status, $post ) {
+	// Update counts for the post's terms.
+	foreach ( (array) get_object_taxonomies( $post->post_type ) as $taxonomy ) {
+		$tt_ids = wp_get_object_terms( $post->ID, $taxonomy, array( 'fields' => 'tt_ids' ) );
+		wp_update_term_count( $tt_ids, $taxonomy );
+	}
+}
 ?>