Hi all,
I have experienced this issue when adding a new addon domain to an existing user.
I have create a new user and added a new domain domain1.tld
Next I have added a second domain domain2.tld to the same user.
After rebuilding the vhost from the "Rebuild Virtual Hosts" menu the second domain "domain2.tld" is using the sub-domain template instead of using the same template used for domain1.tld
From the attached image you can see that the template for addon domain is the subdomain template.