A common problem is that RT will construct the email reply by appending the text in your template to the email header. RFC822 (the email spec) requires a blank line between the end of the email header and the beginning of the email body. If your template text does not add any lines to the header, you must begin it with a blank line. If your template text does add header lines, care must be taken to insert a blank line between the end of the header and the beginning of the body.
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Thank you for your message. Although we have not yet read our letter (we generally don't believe in reading documentation) we are sure that we know what we are doing and that our implementation of your suggestions (which we have not read) will be a complete success.