If when "GSX window" ( which by default is called with Ctrl+Shift+F12, so maybe you changed it ? ), you mean the semi-transparent menu to do commands, that's not really a "GSX window", it's the Simconnect menu window, which is shared by all 3rd party add-ons that have that kind of menu.
We don't have any control over it, the simulator handles it and sometime resizes it and recenter it automatically, even depending on the airplane used.
This post offers some advice how to change the Simconnect window:
http://www.fsdreamteam.com/forum/index.php/topic,16247.0.html