I actually use a different method with my ownCloud setup.
In my vhosts file, I have:
<VirtualHost *:80>
ServerName mydomain.org
Redirect permanent / https://mydomain.org/
</VirtualHost>
Did you get it working ok? (With your .htaccess or otherwise?)
EDIT: This works with subdomains too. For example, I have a virtualhost section for mail.mydomain and cloud.mydomain and they all work perfectly.
Good luck!