No you don't have to clear the CMOs after flashing your BIOS. But you may have to reset your RAM to ECC values as I've found that flashing the BIOS resets RAM to SPD values.
I'm surprised that you have to go through all that BIOS jumper rigmarole. I use Intel's Windows based BIOS update software and it has worked every time with a minimal amount of hassle. Have you tried using this method of updating?
As for the HDD light issue, I've not experienced it since the BIOS v.2507 was released specifically to resolve this problem.
We pushed Intel for the newer bios release. The 2507 did sort the HDD LED problem out but you could not install ANY 64bit O/S with a Quad Core CPU. This error was sorted in release 2618 and now they have updated to 2634. I have installed this on 10+ motherboards now with no issue whatsoever.
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