There are no USB 3.0 Intel
ports on X79 Pro
There are 2 front USB 3 ports with 19 pin header on mobo
There are 4 in back two as #6 and two as #8 in user manual I/O plate diagram
The USB 3.0 are ALL
ASMedia chips which means USB controller must be enabled in onboard devices and drivers loaded and showing in dev manager. No unknown devices with yellow triangle shown in system devices. Look thru all USB entries there and make sure everything looks normal
I dont quite remember, but I think there two ASM entries in dev man - one for ea chip.
USB 3.0 is backwards compatible with 2.0 so flash drives must be USB 3.0 and so stated on purchase package.
And you MUST
disable legacy 3.0 support in bios!!!
You might try a rerun of Intel chipset install pak 9.3.XXXX before anything
since with various bios updates it may need to detect a newer OROM, And I would do a full cmos reset with PSU unplugged even before that.
You can make full copies of your bios pages and settings with a FAT32 stick and pressing F12 to make a screenshot (top middle and bottom) Clearing CMOS loses any profiles.
Just noticed theres a ASM USB firmware update avail
Very strange that yours was working USB 3, then not - could be corrupted bios flash - especially during the convert phase.