If Skype for business is prompting for a password via a web page via as seen below in a fashion duplicating that of the normal login. What you are seeing is the result of Modern Authentication being enabled in the Skype for Business Server.
It is possible to disable modern authentication for Skype for Business either locally for the account via the registry with
Computer\HKEY_CURRENT_USER\Software\Microsoft\Office\16.0\Lync\<user@domain.com>\
DWORD OAuthUsed 1
Change to 0 to disable.
Or globally,
Set-ExecutionPolicy RemoteSigned # Connect to Skype For Business Online # Install Skype For Business Online PS Module # https://www.microsoft.com/en-us/download/confirmation.aspx?id=39366 $credential = Get-Credential Import-Module SkypeOnlineConnector $sfboSession = New-CsOnlineSession -Credential $credential Import-PSSession $sfboSession
For Skype for Business
Online
Set-CsOAuthConfiguration -ClientAdalAuthOverride Disallowed
On-Premises
Set-CsOAuthConfiguration -ClientAuthorizationOAuthServerIdentity ""
Note: Server Updates can take time to be applied and are not immediate.