Hi,
In group policy editor you may add scripts to run at start up. The setting is under Computer Configuration/Windows Settings/Scripts/Startup. You could also use task scheduler to schedule the script to run at start up.
Assign computer startup scripts
http://technet.microsoft.com/en-us/library/cc779329%28WS.10%29.aspx
You may refer to the following article to check the issue:
How Can I Ensure That a Script Runs Only Once on a Computer?
http://blogs.technet.com/b/heyscriptingguy/archive/2007/05/02/how-can-i-ensure-that-a-script-runs-only-once-on-a-computer.aspx
I also recommend you initial a new thread in our Windows Server-Group Policy Forum for further assistance.
http://social.technet.microsoft.com/Forums/scriptcenter/en-US/home
Hope it helps.
Regards,
Summer Deng