My computer has a similar problem and I agree that it is related the M5A99FX Pro R2.0.
I had had a desktop with Asus M5A78L-M USB3 and Kingston SSDnow 300 SSD 240G drive with Windows 10 x64 installed.
Almost a year later, the MB failed, which was replaced with Asus M5A99FX Pro R2.0. Yesterday...