I suggest that you test for either a bad DIMM or a bad (or noisy) DIMM socket. Test with a single DIMM and try using it in each of the DIMM sockets. If it works ok, test with a different DIMM. If all of the DIMMs work fine when used individually and in every DIMM socket, move up to test with two DIMMs, trying them in separate channels and in the same channel.
I hope this helps - and yea, I understand that it is a slow and painful process, but you won't know unless you try...
Thanks for the response. I understand that three short POST beeps is OK, and that three long beeps suggests a memory problem, so I'm still no sure what's going on. Will check logs. Trying all the combinations and permutations of eight DIMMs and eight sockets will certainly be a tedious chore.
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We regret to inform you that the board you are looking support has been discontinued for a while now. As an additional recommendation, test with minimum memory and hardware installed for testing and make sure you have the latest firmware for the board:
Intel® Server Board S5500BC