It would be great if you could play the warranty, but it sounds like your motherboard has been hit by some electric damage (not from the BIOS flash lol).
USB is often first element to go down in such cases.
It could be lightning, particularly if you live in a house not an appartment building and keep your rig on the floor or near some pipes or cables inside a wall, or it could be an electric surge, or hardware/electric failure in one of your USB devices.
Most likely is lightning, and it can even damage rigs that have been switched off and unplugged, where the lightning can have a conduction path via an outside wall or even the floor!
If you live in a detached house you should revise the location of your workstation and ensure that your computer and connected periphals are neither on the floor or next to your wet wall or lightning rod, but if you live in town/in an appartment then you should think about checking the integrity of your electricity installation and of your peripherals.
Of course, USB sockets are also physically fragile, and if there is any peripheral, even keyboard or mouse, directly connected to the motherboard (ie not to a USB port connected via internal cable to the mobo) and that you plug in/unplug daily or often, then the USB socket can be fairly easily damaged, can short circuit, and damage the board...