Due to the UI components the client uses while prompting for Modern Auth, it is not possible for a UI Suppressed client to handle it properly. Therefore it is not supportable to use a UI Suppressed client when signing into a tenant which has Modern Auth enabled.
In some cases this can be helped by disabling Modern Auth on the client side by setting the EnableADAL registry key to 0.
Skype for Business 2016
HKCU\SOFTWARE\Microsoft\Office\16.0\Common\Identity\EnableADAL
Skype for Business 2013/2015
HKCU\SOFTWARE\Microsoft\Office\15.0\Common\Identity\EnableADAL
https://docs.microsoft.com/en-us/skypeforbusiness/manage/authentication/use-adal
Using this key reverts the client to using the Microsoft Sign-in Assistant libraries to authenticate. If there are any issues with that authentication process, then the sign-in will still fail. This has been seen with some 3rd party authentication providers. Reverting to the standard Microsoft Office 365 authentication provider may help avoid this issue.