Couldn't you store window position/size for each window created in a txt file or something? I guess something like:
PHP Code:
<window>@<server name origin>:x,y,w,h
Playerlist@Login:50,50,100,600
Tailor@Unholy Nation:100,150,500,500
And whenever an external window is created, it scans the list for matching criteria and moves it at the correct position. You could even add a script value to enable/disable default positioning.
Also, it seems like input is being stolen away on login to servers. It takes a good 3 or so seconds and clicking the Graal window before I can actually move my player around.