Index: wp-includes/ms-functions.php
===================================================================
--- wp-includes/ms-functions.php	(revision 13549)
+++ wp-includes/ms-functions.php	(working copy)
@@ -50,7 +50,9 @@
 
 	$blogs = $match = array();
 	foreach ( (array) $user as $key => $value ) {
-		if ( false !== strpos( $key, '_capabilities') && 0 === strpos( $key, $wpdb->base_prefix ) && preg_match( '/' . $wpdb->base_prefix . '((\d+)_)?capabilities/', $key, $match ) ) {
+		if ( $wpdb->base_prefix === '' && $key == 'capabilities' ||
+			false !== strpos( $key, '_capabilities') && 0 === strpos( $key, $wpdb->base_prefix ) &&
+			preg_match( '/' . $wpdb->base_prefix . '((\d+)_)?capabilities/', $key, $match ) ) {
 			if ( count( $match ) > 2 )
 				$blog_id = $match[ 2 ];
 			else