Autologin not working with FQDN

I have setup active directory authentication and also autologin (login automatically).

I am using ASPRunner.NET 10.6
The project is compiled using https://servername.org.net/projectname/output'>https://servername.org.net/projectname/output
It works fine when using a non-FQDN URL, e.g. https://servername/projectname/output but it is asking for username/password with a popup window, when using an FQDN URL for the same project e.g. https://servername.org.net/projectname/output'>https://servername.org.net/projectname/output

The behavior remains same when using an SSL or non-SSL URL.
Has anyone came across similar issue?

TIA