I downloaded it again just to confirm, and they are there for me when I open the zip file again. I also now see after looking in trunk and they are not there so that is good news but still confusing how I am getting them. I'm using Sublime to open the files, not really sure how the blank line is getting added.
http://plugins.trac.wordpress.org/browser/wordpress-mu-domain-mapping/trunk/sunrise.php
http://plugins.trac.wordpress.org/browser/wordpress-mu-domain-mapping/trunk/domain_mapping.php
I'm not sure, but I would assume that my problem is experienced by most people. There are hundreds of posts about White space problems and the issues they cause.
Would it be better to remove the closing ?> tags so the problem can't occur and it would follow WP coding standards closer?
Is there an argument for keeping the closing ?> tags?