I loaded the WordPress code into the Eclipse PHP IDE and it immediately detected two blocks of HTML that are embedded into the source and caused errors. I checked an untouched svn version of the source code and it is the same. The problem is also in Wp-mu. You can search for Doctype in functions.php to find the problem. Removing the code also causes a PHP parser problem with an unbalanced function closing tag in function function wp_die the fix for that issue is:
Old code in wp_die:
if ( !function_exists( 'did_action' ) || !did_action( 'admin_head' ) ) :
if( !headers_sent() ){
status_header( $r['response'] );
nocache_headers();
header( 'Content-Type: text/html; charset=utf-8' );
}
New code in wp_die (replace the ":" with "{} open/closing" :
if ( !function_exists( 'did_action' ) || !did_action( 'admin_head' ) )
{
if( !headers_sent() )
{
status_header( $r['response'] );
nocache_headers();
header( 'Content-Type: text/html; charset=utf-8' );
}
}