Running a MSI board now for about a week, all the same hardware as before, and same drivers, with exception of board specific apps and drivers. Only blue screens are related to usb issues, if I have keyboard and mouse in the usb2 ports, can't even make it to desktop, butis fine with usb3 ports, lucky there are 8 usb3s, lol.
Just thought I'd add this last comment so others would know it may well be something other than your graphic drivers.
If I had any hair, X99 would have quickly removed it, lol!