I have a similar Problem
My Specs
i7 Asus Z77 Pro 3 Motherbaord
I got a WD 3TB Hard drive connected to the back USB 3.0 port (tryed both no luck) and from time to time when I logon to windows the drive doesn't connect.. After an initial start up the pc eventually detects it and a pop up displays what i want to do .... like connecting a flash drive or something. If i restart the pc the drive gets recognized next time round but if i shut down immediately the drive continues to be unrecognized.
If I perform a restart when the drives not detected the next time I boot it works fine for the next 3 - 4 bootups but then eventually it's not detected again.