I'm having the same problem here... Everythigns works fine, until the point when I have to create a subdomain, instead of using user:group from the account I'm using to create the subdomain, it uses root:root. So we can't upload or install anything until we go to the Admin panel and use the "Fix permissions" module and correct the permissions for the account that created the subdomain. So no longer an automated task for the user.
Any thoughts on this one? Any help would be appreciated.
Thanks!