Is there anything I can do with this? Is this some sort of bug? I must admit that it is pretty confusing and irritating that I have to close the second, not operative "copy" of main Skype windows (that appears after each click on Skype notification) to be able to interact with Skype in any way.
We have disabled the use of Microsoft apps such as mail, Xbox calendar and skype. However, skype likes to start itself with windows in the task tray now, so whenever a user logs on, they are greeted with the "This app has been blocked by your system administrator. Contact your system administrator for more info" screen that takes up the whole screen, slightly annoying for users.
Deleting the Lync value in HKEY_CURRENT_USER\SOFTWARE\Microsoft\Windows\CurrentVersion\Run(However I've learned that there is no lync key because this is different from skype for business, this is a Microsoft app)
Unfortunately, neither of these skype apps are in the registry which is the strange thing. However, when I log in I still get the message pop up on one of the machines. So I checked the event viewer and I am receiving a warning level event (event ID: 866) with the following message "Access to C:\Program Files\WindowsApps\Microsoft.SkypeApp_15.61.100.0_x86__kzf8qxf38zg5c\Skype\Skype.exe has been restricted by your Administrator by location with policy rule ee6b0825-191e-4de7-b4ed-c686f12f299a placed on path C:\Program Files\WindowsApps\Microsoft.SkypeApp*."