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Hopefully the BIOS update will fix it, but something I haven't seen anyone mention and I've hit it before when using HDMI - when your GPU is in place, is the HDMI port centred in the gap when you look from the rear? I've had a couple of times when the port isn't centred and so the plastic surround on the HDMI cable hits the metal strips between PCI slots, stopping it going in far enough to make a connection.
Solutions range from getting an HDMI with a thinner plastic surround on the end, filing the plastic a little or melting the plastic a little with a lighter to make it fit, but I ended up loosening the screw holding the GPU in place, apply a little pressure to the card to centre the HDMI port, then do the screw up to hold the card in that place.
Like I said, hopefully it's just a BIOS update but just in case it's not thought it best to mention this. Good luck.