Index: wp-includes/widgets.php
===================================================================
--- wp-includes/widgets.php	(revision 11684)
+++ wp-includes/widgets.php	(working copy)
@@ -965,13 +965,15 @@
 		$sidebars_widgets = get_option('sidebars_widgets', array());
 	} else {
 		if ( empty($_wp_sidebars_widgets) )
-			$sidebars_widgets = get_option('sidebars_widgets', array());
-		else
-			$sidebars_widgets = &$_wp_sidebars_widgets;
+			$_wp_sidebars_widgets = get_option('sidebars_widgets', array());
+
+		$sidebars_widgets = $_wp_sidebars_widgets;
 	}
 	$_sidebars_widgets = array();
 
-	if ( !isset($sidebars_widgets['array_version']) )
+	if ( isset($sidebars_widgets['wp_inactive_widgets']) )
+		$sidebars_widgets['array_version'] = 3;
+	elseif ( !isset($sidebars_widgets['array_version']) )
 		$sidebars_widgets['array_version'] = 1;
 
 	switch ( $sidebars_widgets['array_version'] ) {
@@ -1024,20 +1026,29 @@
 					}
 				}
 
-				// 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 = $_sidebars_widgets;
 				unset($_sidebars_widgets);
 			}
 
+			$sidebars_widgets['array_version'] = 3;
 			if ( $update && is_admin() )
 				update_option('sidebars_widgets', $sidebars_widgets);
 	}
 
+	if ( !is_admin() )
+		$_wp_sidebars_widgets = $sidebars_widgets;
+	
 	if ( isset($sidebars_widgets['array_version']) )
 		unset($sidebars_widgets['array_version']);
 
@@ -1086,9 +1097,8 @@
  * @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 {
@@ -1119,13 +1129,14 @@
 				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);
 	}