I have never heard of a BIOS update remapping the LED pin-outs. It would be pretty hard to do as it is a physical interface. BTW, it fades away as the residual power that is stored in your motherboard's components dissipates.
Not to add any insult, but are you 100% sure it worked as intended before the BIOS update? Please don't take offense, but little things like that are often overlooked and are coincidental with users noticing a problem. Every true geek has done this to themselves, including me.