Same here, after upgrading with the latest 10.4.3 package they are getting this message, but only when trying to use IIS Windows Authentication, the prompt that pops up if you hit the server remotely and manually enter your user and password. I confirmed with 2 accounts which are part of the Directory Server Administrators group.

If we login to the server OS and hit the site with localhost/LFDS then we get auto logged in and it works. So only a problem with remote connections and this client said it was working until I upgraded just this weekend.

I just encountered the same issue on a system running LFDS 10.4.5.623 and resolved it with this...

https://support.laserfiche.com/kb/1014252/windows-authentication-fails-due-to-an-incorrect-automatic-setting-in-the-usersettings-config-file

Side note... 

• on a system initially deployed with 10.4.5.623, the problem was present (the user experienced the error noted, and the entries in the settings file were mixed, some with computer name, and some with alias).  Updating all the entries to the computername resolved the issue.  
• on a system initially deployed with an earlier version (I'm unsure which version), and then upgraded, we did NOT have the problem.  No users experiencing the error and all the entries in the settings file were populated with the computer name. 

This leads me to believe that a fresh install of affected versions will introduce the problem when they create the settings file noted in the KB... but UPGRADES to affected versions may not, as they may leave an existing (and correct) settings file untouched.  

For us, this explained why we saw the problem on systems that were absolutely identical... except how they arrived at 10.4.5.623 (one a fresh install, and one an upgrade).