I just finished reading the FAQ regarding:
Why doesn't my script work on a locked workstation?One thing that I didn't see mentioned was to run the AUTOIT on a separate machine (either real or virtual) and RDP into the second machine.
One can achieve security in such a setup by locking the local machine while AUTOIT continues to run on the remote machine.
The remote machine doesn't seem to lock if AUTOIT is doing sends and mouse moves.
Phil