If you have admin privileges, then you can run AutoHotKey "As Administrator" and it will work with all programs, including those with admin privileges.
If not, then the only way I know if is to open the Windows registry and make the changes that way. There is a program out there called RemapKey that has a graphic you can use to drag and drop your keyboard changes. When you click "save" it saves your changes, and then you can log off and log back on.
My problem now is I just got a job with a company that has tight security procedures and I don't know if they'll even let me use AutoHotKey. I hate it that the government has taken over so much of the software development business. It seems that private businesses (mostly financial...