It should keep the line breaks, unless you are viewing the html version. Are you using a text-only email client?
I think we replace <br> tags with line breaks for the text only version... try adding <br> tags where you want line breaks.
The way it works is that if you view the email with a viewer that supports html, you get the html version, if you are using plain-text only client, you get the plain text version.
If you aren't happy with that I can work with you and show you a couple of ways to work around the problem in a support ticket. Let me know if you think that is necessary and we can add an incident for you.