I've recently installed ArcGIS for Server 10.3 and also Portal for ArcGIS (first time using Portal). I've installed web adapter and also enabled SSL (currently using the self-signed certificate). In Portal I have also added in several of my dynamic map services and shared these with everyone. I have also created a map using these map services and the map is also shared with everyone. The map opens and displays fine, but when I click on a feature to open the pop-up I get a Sign in box asking for a username and password. If I cancel and close this box everything works fine - but I'm not sure why the Sign in keeps appearing? Interestingly, if I add the same services to a map in AGOL this doesn't happen.
In a possible related problem, I have tried to change map service sharing properties in ArcGIS Server Manager but get the error that I am not signed in to a Portal, however, under Services > Sharing I am not able to change the portal and service URL addresses. When I alter them and click save, nothing happens.
Two possible causes that I can think of are that I don't have a signed certificate installed and because of this I cannot federate ArcGIS for Server with my Portal.
Can anyone shed any light on these issues for me?
I would be interested to see what kind of requests are going on behind the scenes when this authentication prompt comes up when you're trying to view pop-ups. Could you install Fiddler (http://www.telerik.com/download/fiddler) and capture some traffic while this issue comes up? Since you are using SSL, you may need to go to Tools>Fiddler Options>HTTPS and check "Decrypt HTTPS traffic" to get useful captures. I am interested in where the authentication request is coming from, the ArcGIS for Server service's URL or your Portal. This can also help point us in the right direction on troubleshooting.