The Skype for Business (formally Lync) window suddenly appears as the top most window stealing the focus from the program you were previously using. This behavior may begin to occur out of the blue.
There is a setting in the options that is meant to give Skype for Business the focus when the program starts (located at Options->Personal->Start the app in the foreground). For reasons unknown to me, this setting can cause Skype for Business to take the foreground focus every half minute or so (where it should only be doing it when the program starts). It's possible that the client is restarting itself or some mechansim is reloading and triggering this event (I haven't checked to see if the PID changed after each occurance). The solution is to disable this setting.