the opus doesnt cut the power to the 5v line unless your batery level drops.
Go into the device manager when the items arent working and see if they show up and if they do see if they are active or dissabled. You might need to use something like devcon to dissable and enable them although this is usually only needed for hibernation. Better option that will save your batery as well is to use Randos circuit to cut the 5v to the mobo if you intend to shut down all the time. I havent used this myself but dont think this would cure the hibernation issues so I guess the ultimate is to use the circuit and Devcon along with hibernate triger and some scripts. Remember the scripts and Devcon only disconect the software and not the voltage so it isnt a replacement for the relay and diods.