Index: wp-admin/includes/theme.php
===================================================================
--- wp-admin/includes/theme.php	(revision 17487)
+++ wp-admin/includes/theme.php	(working copy)
@@ -181,6 +181,9 @@
 			if ( false !== strpos($basename, '/') )
 				continue;
 
+			if ( 'functions.php' == $basename )
+				continue;
+
 			$template_data = implode( '', file( $template ));
 
 			$name = '';