A similar issue with adding extra 0D symbols to the message headers by kav-qmail has been already reported and fixed. The fix will be available in the upcoming Critical Fix (kav4lms 5.6 CF1). Its technical release is currently planned for the end of March.
This known problem, however, was noticed with unix local delivery. I'm not sure that it's exactly the same case you've reported here. I can provide you the fixed version of the application before it's official release so that you'll be able to verify that your case is fixed as well.
By the way, according to RFC, the line delimiter for SMTP messages is the CR+LF sequence. Any bare LF or CF are considered as malformed symbols. D.J. Bernstein, the creator of qmail, is known as a strict standard purist, so I wonder how can you even send messages with bare LF symbols (see his special article on this issue:
http://cr.yp.to/docs/smtplf.html). If the mail client converts bare LFs to standard CRLF pairs while sending the messages by SMTP to qmail, they should go further to Exchange in the same form via SMTP as well, so I just cannot imagine how can Exchange rely on this format at all... This case (transferring messages via SMTP) differs in this sence from local delivery where the delivery happens using unix native line feeds rather than SMTP standard CRLF pairs...
Anyway, I'd like you to verify the case on the next build.