I hope I got a solution or a workaround for your problem.
http://docs.moodle.org/22/en/Email_processing
Infos are in chapter: "Email confirmation or registration words, and how to edit them"
I changed in moodle.php the text for the field "paymentthanks". I made the changes directly in moodle and not in a text-editor. The changes are not yet tested, but I hope I have the time to do it within the next days.