Index: wp-includes/post-template.php
===================================================================
--- wp-includes/post-template.php	(revision 12371)
+++ wp-includes/post-template.php	(working copy)
@@ -164,7 +164,10 @@
 function the_content($more_link_text = null, $stripteaser = 0) {
 	$content = get_the_content($more_link_text, $stripteaser);
 	$content = apply_filters('the_content', $content);
-	$content = str_replace(']]>', ']]>', $content);
+	// a shortcode might have overridden $wp_query by calling query_posts()
+	global $wp_the_query;
+	if ( $wp_the_query->is_feed )
+		$content = str_replace(']]>', ']]>', $content);
 	echo $content;
 }