Só para ter certeza, você tentou o seguinte usando #IfWinActive para a tecla de atalho script.ahk?
#NoEnv ; Recommended for performance and compatibility with future AutoHotkey releases.
SendMode Input ; Recommended for new scripts due to its superior speed and reliability.
SetWorkingDir %A_ScriptDir% ; Ensures a consistent starting directory.
SetTitleMatchMode, 2
#IfWinActive script.ahk
$>^s::
Send ^s
Sleep, 100
Reload
Return
#IfWinActive, ahk_class VirtualConsoleClass
LCtrl::AppsKey