I have an install of Portal 10.4.1 which I have set up with Windows authentication through IIS and the web adaptor. I have set our enterprise details through the identity store. I can successfully add users. I'm seeing strange behaviour when clicking through to web app builder apps from the front page of the portal. The web app page comes up blank - if you go to the console it says there is an an unterminated string error when it passes through the username details as JSON. It gets to the full name and then stops. The only thing I can think is that the cn in our directory have the format 'Firstname Lastname (username)' - I was wondering if it was somehow getting confused with the space and bracket after the lastname. The character number that it's failing at seems to match up to this. The other strange thing is that it's intermittent. We have two realms, and sometimes it works in one and not the other, sometimes neither, and sometimes it'll be fine for a while and then fail.
Also, there's probably a related question in how to best set up the realms - could split this into another discussion. At present I seem to need to set up two accounts for the same user - username@realmA and username@realmB. I'm wondering if this is maybe part of the problem.
We are experiencing similar behavior at Portal 10.4.1 with IWA through IIS and web adaptor where users encounter blank pages when opening the Portal home page or when opening web applications. In our case, sometimes the page never comes up and sometimes it will come up although it can take anywhere from 30 sec to 2 minutes. Sometimes the pages come right up fine with no performance delay. We have three Portals and have experienced it on all three, but not necessarily at the same time. It is intermittent on all three of the Portals, just as you described. If you find a solution, please post it.