I had the same issue with wpmudev. I only want to use the domain mapping plugin but the premium cost of 45 dollars a month is not worth it. I have switched to this plugin and took me less than a minute to switch. I uninstalled the old plugin, installed domainer, mapped the domains and it works fine.
When you use ssl on your website and want to force to show the https:// then you have to add the following code in your .htaccess. In the wpmudev you can selected this option. With domainer you have to do it manually.
RewriteEngine On
RewriteCond %{HTTPS} !=on
RewriteRule ^/?(.*) https://%{SERVER_NAME}/$1 [R,L]
