Index: wp-admin/menu-header.php
===================================================================
--- wp-admin/menu-header.php	(revision 23612)
+++ wp-admin/menu-header.php	(working copy)
@@ -87,7 +87,7 @@
 			$menu_file = $submenu_items[0][2];
 			if ( false !== ( $pos = strpos( $menu_file, '?' ) ) )
 				$menu_file = substr( $menu_file, 0, $pos );
-			if ( ! empty( $menu_hook ) || ( ('index.php' != $submenu_items[0][2]) && file_exists( WP_PLUGIN_DIR . "/$menu_file" ) ) ) {
+			if ( ! empty( $menu_hook ) || ( ( 'index.php' != $submenu_items[0][2] ) && file_exists( WP_PLUGIN_DIR . "/$menu_file" ) && ! file_exists( ABSPATH . "/wp-admin/$menu_file" ) ) ) {
 				$admin_is_parent = true;
 				echo "<a href='admin.php?page={$submenu_items[0][2]}'$class $aria_attributes>$arrow<div class='wp-menu-image'>$img</div><div class='wp-menu-name'>$title</div></a>";
 			} else {
@@ -98,7 +98,7 @@
 			$menu_file = $item[2];
 			if ( false !== ( $pos = strpos( $menu_file, '?' ) ) )
 				$menu_file = substr( $menu_file, 0, $pos );
-			if ( ! empty( $menu_hook ) || ( ('index.php' != $item[2]) && file_exists( WP_PLUGIN_DIR . "/$menu_file" ) ) ) {
+			if ( ! empty( $menu_hook ) || ( ( 'index.php' != $item[2] ) && file_exists( WP_PLUGIN_DIR . "/$menu_file" ) && ! file_exists( ABSPATH . "/wp-admin/$menu_file" ) ) ) {
 				$admin_is_parent = true;
 				echo "\n\t<a href='admin.php?page={$item[2]}'$class $aria_attributes>$arrow<div class='wp-menu-image'>$img</div><div class='wp-menu-name'>{$item[0]}</div></a>";
 			} else {
@@ -150,12 +150,12 @@
 
 				$title = wptexturize($sub_item[0]);
 
-				if ( ! empty( $menu_hook ) || ( ('index.php' != $sub_item[2]) && file_exists( WP_PLUGIN_DIR . "/$sub_file" ) ) ) {
+				if ( ! empty( $menu_hook ) || ( ( 'index.php' != $sub_item[2] ) && file_exists( WP_PLUGIN_DIR . "/$sub_file" ) && ! file_exists( ABSPATH . "/wp-admin/$sub_file" ) ) ) {
 					// If admin.php is the current page or if the parent exists as a file in the plugins or admin dir
-					if ( (!$admin_is_parent && file_exists(WP_PLUGIN_DIR . "/$menu_file") && !is_dir(WP_PLUGIN_DIR . "/{$item[2]}")) || file_exists($menu_file) )
-						$sub_item_url = add_query_arg( array('page' => $sub_item[2]), $item[2] );
+					if ( ( ! $admin_is_parent && file_exists( WP_PLUGIN_DIR . "/$menu_file" ) && ! is_dir( WP_PLUGIN_DIR . "/{$item[2]}" ) ) || file_exists( $menu_file ) )
+						$sub_item_url = add_query_arg( array( 'page' => $sub_item[2] ), $item[2] );
 					else
-						$sub_item_url = add_query_arg( array('page' => $sub_item[2]), 'admin.php' );
+						$sub_item_url = add_query_arg( array( 'page' => $sub_item[2] ), 'admin.php' );
 
 					$sub_item_url = esc_url( $sub_item_url );
 					echo "<li$class><a href='$sub_item_url'$class>$title</a></li>";