A Windows Authentication prompt is shown after previously successfully logging into the Qlik Sense Enterprise on Windows hub using a Virtual Proxy (with a custom prefix). The Virtual Proxy does not use NTLM.
This issue is known (QB-20236) and a fix is currently being developed by R&D.
The issue has been identified in that the following files are attempting to use the default Virtual Proxy:
react.production.min.js
react-dom.production.min.js
It appears to be an issue with the cookie being used. If the default Virtual Proxy (using Windows Auth) cookie is within the cache it works. If it is not, you will get the pop-up.
See img 1 as an example, you see the requested files react.production.min.js, and react-dom.production.min.js throwing a 401 error.