I am having similar problems. I just built a PC with an Asus M5A78L USB3. (Heard good things but the mb stinks, must of been people buying cheaper CPUs and other parts old OS ) installed a 250GB SSD and a 2TB HDD. I installed Windows 8 Pro and right away I had problems, both drives showed up but then my 2TB disappeared completely. I checked all the settings, services, components, registry and device manager there all fine. I also am having problems using the USBs both the 2 and 3.0. I did mechanic work to check drives but it doesn't recognize the second drive either. My last option is to go into the BIOS and see if they're any settings or updates I need but the only usb that works is my keyboard and doesn't work till Windows sign in; In fact I have to use a onscreen keyboard just to login. Then the keyboard works. I also installed tons of legacy hardware just in case. This is my first time here and would really appreciate the help and to keep going to give back the favor. Oh a mysterious thing is that no program or anything will pick up the second hard drive but if u expand in device manager, then go to views and click on show hidden devices then I can see it but grayed out.