I have several shortcuts set to start up with windows 8.1 in the shell:startup folder. I have set them all to minimize, however none of them do. They all start regularly except for Skype which I don't have in that directory. If I test out the short cuts by themselves they start minimized but not when windows starts up.
I am running Windows 8.1 on a 2012 5.1 Mac Pro under Bootcamp.