Since you mentioned bootup, and not at user logon, using the startup folder or the Run key will not work as they require a user logon to take place. If you really want to use the Registry, you need to use the following key:
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunServices or RunServicesOnce
Note that the Run key is also ignored in Safe Mode. However, I would suggest a Windows Service. They are designed to be started when the system starts, and will be running when a user logs on and will remain running after a user logs off. They can easily receive for logon/logoff events. If you need finer control the point where your application starts, I think you would have to go the driver route. Peace!
-=- James
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