I had a bunch of problems with this myself with plain text e-mails from Linux systems (just text files shoved out using /bin/mail). I did bunches of translation and tried every line ending I could to get what I wanted. I think I eventually stumbled across Line breaks are removed in posts made in plain text format in Outlook. I don't know if that will help (especially since you are using MIME e-mails), but it's worth a look.