With Cyber Science 3D version 5.2.2638.1 to 5.2.2638.4 or newer, 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.