The USB drive I am attempting to use now is the same USB drive I had used before, and back then in worked. The contents of the drive have not changed at all. I have also tried 4 different USB drives from different manufacturers and they all suffer from the same problem.
The BIOS appears to see the USB drive, as when I go under "HDD boot order" I can see my USB drive there. Pressing F12 to invoke the boot menu and selecting USB-HDD will cause it go boot from the normal HDD and into Windows. Pressing F12 and selecting Hard Disk and then selecting the USB drive on the sub menu will cause it to say "Boot from CD/DVD", and then actually attempt to boot from CD/DVD.
I tried every single USB port I got and I could not get QFlash to see the USB drive, even though it was shown on the BIOS.
The only way I found of flashing the BIOS was by using @BIOS from the OS.
The only difference I noticed after the FD update was that it is now much faster to detect the IDE devices at startup (it ALWAYS used to take more than 15 seconds just on the IDE devices, it now takes about 3-4 seconds).
Ever since I bought the board I would sometimes have a problem where it would get stuck at POST if I had the SATA devices set to AHCI. Wouldn't even allow me to enter the BIOS at all. The solution was to remove the SATA connector from the HDD, enter BIOS, set SATA to IDE, plug HDD back in, remove all partitions from HDD, go back into BIOS and set it back to AHCI. Since deleting the partition table always fixed the issue, I never thought it would be a problem with the motherboard itself.
I'm more than happy to try the steps mentioned above, but those seem to be directed mostly at the issue with the USB booting directly. Do you think all the other issues are also related and could all be fixed with a prolonged CMOS clear?