Strangely, there is only one clean way to fully shut down an RT box: do a software reboot, either from MAX or the LV project, or with the Reboot Controller VI that ships with RT. If you wait until the target gets to the BIOS screen and then turn it off before it boots RT, that is the cleanest way to shutdown, because RT will have given everything running on the target (such as drivers, etc) a chance to cleanly shutdown and cleanup whatever it is doing. The disk cache will be flushed, and things will be as clean as they can get.