I've worked around extensively on that exact problem, and I think I've finally got the answer. The value that must be passed to the user32 library is "12" (decimal) for the system to shut down silently. Really, that value means "power off", while the "5" passed when you select the "shut down" option means "force shut down", which exits windows but does not power off the PC.
(More info at http://msdn.microsoft.com/library/default.asp?url=/library/en-us/sysinfo/base/exitwindowsex.asp )
So, what you must do is either adding an option to the "Exit Windows..." vi giving the correct value or directly passing the value "12" into the "ReturnCode" field of that dll.
I attach the modified VI which powers off the system straightforward (NT-2000-¿XP?). Hope i
t works fine.
Felipe