I successfully got a certificate on my owncloud installation using the webroot plugin.
First it didn’t work, but then I figured out i had to add
RewriteRule ^\.well-known/acme-challenge - [L]
to the ownclouds .htaccess mod_rewrite section. This prevents the authentication request being redirected by ownclouds carddav/caldav parts…
I don’t known if it helps for your current issue, but it may help later.