If "Always on top" is enabled, the XCenter will always remain on top of all windows on the system. This is a "really-always-on-top" setting and will affect the entire system.

Hint: If you don't like this setting, assign an object hotkey to the XCenter on its "Object" page. If you then press that object hotkey and the XCenter is already open, it will be resurfaced to the top of all windows.