Problem Description :

Multiple users from site not able to access eB Web after migrating eB License and getting Windows Security Window pops up with which fails user credentials

Solution :

This seems to be issue with IIS where Windows Authentication is set to disabled and thus does not allow user to login with system credentials in Windows Security box

Enable Windows Authentication in IIS for required web server and that web app as per steps below

Start > Type IIS > Open IIS manager > and expand server name from right hand pane

Select the site and in Authentication window you see Windows Authentication - Enable it

And restart the IIS