"Windows do not recognize USB devices until I get to a desktop or login screen inside of Windows."

I know why but have no solution. Let's go with what I know.

Prior to Windows loading the BIOS has code to emulate PS/2 keyboard and such until Windows gets on its feet and loads a few drivers. Including the ones for this card. Since the BIOS can't use these ports, any USB keyboard on the PCI card won't work till later.
Bob