Mail::Mailer is a pretty crufty old piece of code. I would recommend using Mail::Sendmail (which is pure perl), or even Net::SMTP (which is a little more low-level, but fine if you're playing around inside your localnet). I have used both of these modules to talk to Lotus MTAs, and they work just fine, and I can diddle the headers however I want (with reason).

For instance, I often set the From: line to be the name of the application that is generating the message, and set the Reply-To: to the person who is capable of taking care of what issues may be raised by the contents.