With Cyber Science 3D version 5.2.2638.1 to 5.2.2638.4, Cyber Science will change from fullscreen mode to windowed mode when zView is enabled. The desktop shortcut is missing the command argument -fullscreen 0.
This issue is resolved by updating to Cyber Science 3D version 5.2.2638.6.
As another workaround, you can add the command argument screen-fullscreen 0 into the shortcut properties. The article here steps you through how to modify command arguments in a shortcut.