If you’re using the Office 2013-based version of the Lync / Skype for Business client, patch version 15.0.4711.1000 (April 2015) introduced the ability for it to show either the Lync 2013 UI (skin) to the user, or the Skype for Business one. The csClientPolicy setting “EnableSkypeUI” dictates which UI will be presented, and this is passed in-band to the client when the user signs-in.
The client only tests this value on launch – not when the user signs in – so for the client to show the correct UI it will need to be restarted each time you switch users/sites. You can have bounSky do this for you automatically by checking the box “upon successful sign-in … restart the client” under Setup / Options.
Note that the Office 2016-based version of the client no longer includes the Lync 2013 UI, and will always display the SfB UI regardless of the user’s csClientPolicy “EnableSkypeUI” setting. Checking “upon successful sign-in … restart the client” serves no purpose for users of the Office 2016 client.