hi , same problem have and when is not in compatibility setting but is with this situation
portal is 10.4
added to domain
installed and using web adaptor
turned on Active Directory Authentication
SSL certificate ( with certificate authority ) and name is FQDN
and when we add the url of portal to local intranet ( with FQDN and without FQDN)
when open home of portal is ok but when click in top Navigation menu show same error.
we show the link in url is appended .
example we are in home tab and click on gallery the resuts is error and url is example modified:
https://portal.domain.com/arcgis/home/https://portal.domain.com/arcgis/home/gallery.html
when using only direct links working.
when removing from local intranet site working without this problem.
we tested to add separately and in trusted sites and local intranet - same results.
We think the problem is in the code of Top Navigation Menu buttons , because inside not showed this problems.
example when we are in map viewer ( in portal ) and using in top menu not have this problem all work