Você pode tentar fazer com que seus scripts sejam executados como Admin
if not A_IsAdmin
{
Run *RunAs "%A_ScriptFullPath%" ; Requires v1.0.92.01+
ExitApp
}
Veja o link
ou tente ativar a interação com programas administrativos usando EnableUIAccess :
Modifies AutoHotkey.exe to allow scripts to do the following even while UAC is enabled:
* Interact with windows of administrative programs without running the script as administrator.
* Use SendPlay.
Source: http://www.autohotkey.com/board/topic/70449-enable-interaction-with-administrative-programs/