Seems like the bios screwed the device ID, so that is can't be identified as an ATI card anymore. Assuming your nVidia card is in your upper slot, and your ATI in the next slot, have you tried the command:
atiflash.exe -p 1 -f <biosname>
That should force a flash on the secondary card.
Edit: Make sure you use an up to date atiflash version. Older version didn't support 128kb bioses, so it might only flash the first 64kb of the bios, resulting in corrupted bioses.
he already tried force flashing the first time (-f -p 0/1 doesn't matter which order i think).
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