My system won't recognize the on-board 3.0 ports that come in the motherboard, after the BIOS being flashed and the 3.0 Drivers being installed (uninstalling the ports,restarting etc). And this is all after formatting my system, the 3.0 ports worked fine before.
More about :asus p8p67 pro rev usb ports recognized
i am guessing you went to the device manager and looked for the "USB 3.0 Hub" there and thats why you are saying it wont recognize the ports. If you didnt do that yet, try it. if its not there, Check the bios Options.
in BIOS in the section about where you want to start up from (HDD, External, Optical Drive Etc.) there is an option for USB 3.0 Monitoring On/OFF, (it can be somewhere else, just look around the bios option. i didnt try this on an ASUS, but i did try it on Dell, Toshiba, HP/Compaq, and they have an option there.)