At the bottom of the file:
/includes/languages/english/modules/shipping/flat.php

you will see:
Code:
define('MODULE_SHIPPING_FLAT_TEXT_TITLE', 'Flat Rate');
define('MODULE_SHIPPING_FLAT_TEXT_DESCRIPTION', 'Flat Rate');
define('MODULE_SHIPPING_FLAT_TEXT_WAY', 'Best Way');
?>
try removing the closing php tag that I highlighted in RED and see if that corrects the problem ... this sounds like you have space(s) or blank line(s) at the bottom of it causing this issue ...