I have been working on windows automation and monitoring.
What exactly happens when I lock the screen of a windows machine?
I am working with Windows 7 at
I don't know the details, but I believe the lock screen constitutes a separate "desktop" and maybe also a separate "window station" (as I understand it a window station is merely a container for desktops). The MSDN section on window stations should hopefully be useful: http://msdn.microsoft.com/en-us/library/windows/desktop/ms687098%28v=vs.85%29.aspx
In order to access a desktop, you will need to use the regular windows api's from a thread that is on that desktop. SetThreadDesktop would probably be the easiest way to do that in C, as long as the desktop isn't on a different window station.
Unfortunately, this is already difficult for a regular privileged application, and using AutoHotkey complicates it even more. Since you don't have control over threads or over process initialization, you will probably have to create a new process in the other desktop (you can do this using the CreateProcess API, which appears to have a wrapper available for AHK to which you can supply a desktop name: http://www.autohotkey.com/forum/topic1952.html). Your process will need special privileges to do this; I'm not sure that even running as Administrator is enough.