I've managed to upgrade the HBA firmware after installing it in a different system and can confirm that the card is in fact working. Additionally, I should point out that I was wrong about the model number, it's actually an LSI 3442R-E SAS HBA (which is the one listed on Intel's compatibility list).
I have an FC HBA that I'll test in the system when I get home from work as I'm starting to think that ALL the PCI-E ports are not working... Unless anyone else has suggestions I'm not sure what else to do other than just return the board for a replacement.
Still no ideas?
Looks like I should modify the title to "S5500BC not detecting LSI HBA" as the FC HBA I installed worked just fine. I have tried putting the HP SC44Ge firmware on this card too without any success.
I called Intel who said to try with quiet boot and NIC ROMs disabled, however it STILL doesn't detect the HBA.
Now that I have some hard drives plugged in (via expander card) I can see that the HBA is registering activity from the drives, so it is definitely functional. It's starting to look like there might be a firmware issue with the S5500BC and Intel may have only tested with newer versions of this card (there are B1, B2 and B3 versions of the HBA with mine being the B1). A colleague has an SC44Ge (3442E-R) working in a personal Intel socket 775 server board.
I gave up on this and bought an Adaptec 2045 (also listed as compatible, but who knows what will happen!). Intel support are trying to source a B1 LSI SAS 3442E-R to retest it with an S5500BC and if they have the same issue I experienced I would expect them to release either a revised compatibility list or firmware update to fix the problem.
Personally, I think the board is screwed. I just plugged an RMM3 into it and that isn't detected either. Possibly the single most frustrating piece of hardware I have owned, considering how many times I checked and double checked compatibility lists to ensure that these exact problems didn't occur. I'll be calling Intel to raise another case for the RMM3 tomorrow, but if they don't have a good answer for me I'll be demanding a refund.
Very disappointed, Intel! I won't be recommending these boards to anyone, especially considering I don't appear to be the only person experiencing problems.