Using Joomla 3.6.2 and CiviCRM 4.7.11 and experiencing duplicate emails in CiviMail. We've tested with contacts with same email address + in same group, resulting in 2 emails received. We've also tested with contacts with same email address though in separate groups, resulting in 2 emails received. Attached image demonstrates 2 separate groups, each with 2 contacts in each group (different first/last names, though same email addresses... so 2 unique email addresses).
CiviMail component settings includes "CiviMail dedupes email addresses by default" as checked.
Also just tried to use the connections to provide a site profile assuming that might help troubleshoot this. Noticed in the image that the site url contains "administrator" twice. Perhaps this is a separate issue or maybe it's related?