So, after looking into this.
Apparently windows sends a CtrlBreak (aka VK_CANCEL, or VK_03) when you do either Ctrl+Pause (or Ctrl+Scroll?), not sure why AHK can't intercept that but oh well...
When the game receives this key code, it calls MoveWindow(param_1,0,0,0x280,0x1e0,1);
I guess this...