Index: wp-includes/widgets.php
===================================================================
--- wp-includes/widgets.php	(revision 11673)
+++ wp-includes/widgets.php	(working copy)
@@ -967,7 +967,7 @@
 		if ( empty($_wp_sidebars_widgets) )
 			$sidebars_widgets = get_option('sidebars_widgets', array());
 		else
-			$sidebars_widgets = &$_wp_sidebars_widgets;
+			return apply_filters('sidebars_widgets', $_wp_sidebars_widgets);
 	}
 	$_sidebars_widgets = array();
 
@@ -1024,10 +1024,16 @@
 					}
 				}
 
-				// Assign to each unmatched registered sidebar the first available orphan
-				unset( $sidebars_widgets[ 'array_version' ] );
-				while ( ( $sidebar = array_shift( $sidebars ) ) && $widgets = array_shift( $sidebars_widgets ) )
-					$_sidebars_widgets[ $sidebar ] = $widgets;
+				// move the rest to wp_inactive_widgets
+				if ( !isset($_sidebars_widgets['wp_inactive_widgets']) )
+					$_sidebars_widgets['wp_inactive_widgets'] = array();
+				
+				if ( !empty($sidebars_widgets) ) {
+					foreach ( $sidebars_widgets as $lost => $val ) {
+						if ( is_array($val) )
+							$_sidebars_widgets['wp_inactive_widgets'] = array_merge( (array) $_sidebars_widgets['wp_inactive_widgets'], $val );
+					}
+				}
 
 				$_sidebars_widgets['array_version'] = 3;
 				$sidebars_widgets = $_sidebars_widgets;
@@ -1086,9 +1092,8 @@
  * @return array
  */
 function wp_convert_widget_settings($base_name, $option_name, $settings) {
-	global $_wp_sidebars_widgets;
 	// This test may need expanding.
-	$single = false;
+	$single = $changed = false;
 	if ( empty($settings) ) {
 		$single = true;
 	} else {
@@ -1110,7 +1115,7 @@
 			$sidebars_widgets = get_option('sidebars_widgets');
 		} else {
 			if ( empty($GLOBALS['_wp_sidebars_widgets']) )
-				$GLOBALS['_wp_sidebars_widgets'] = get_option('sidebars_widgets');
+				$GLOBALS['_wp_sidebars_widgets'] = wp_get_sidebars_widgets(false);
 			$sidebars_widgets = &$GLOBALS['_wp_sidebars_widgets'];
 		}
 
@@ -1119,13 +1124,14 @@
 				foreach ( $sidebar as $i => $name ) {
 					if ( $base_name == $name ) {
 						$sidebars_widgets[$index][$i] = "$name-2";
+						$changed = true;
 						break 2;
 					}
 				}
 			}
 		}
 
-		if ( is_admin() )
+		if ( is_admin() && $changed )
 			update_option('sidebars_widgets', $sidebars_widgets);
 	}