You formatted both disks or just the one disk you installed the OS on? In other words you would have had to run the format twice.
As for your USB ports I would try and re-install them first.
If that doesn't work then make sure you have the latest chipset firmware for your mobo.
I am not sure where the option is in your BIOS, but it should be pretty obvious.
Forgot to ask, but they did work before correct?
***I would suggest going here
and making sure you have the most current hardware drivers/firmware that is applicable to your system except Beta stuff. And make sure you select the operating system that you are using, that link has XP stuff.