Hello,
You can control windows programs, by for instance ActiveX, check the examples shipped with LabVIEW - Comunicating with external applications - ActiveX.
In this link: http://digital.ni.com/public.nsf/allkb/80878EF7B8E5FA0786256AB9000151B9, you can find a exit / reboot windows function, to restart with a program, you can, for instyance copy a shortcut to it to the startup menu.
Hope this helps,
Paulo