Not 100% without looking at it directly, but the first 2 things that come to mind are CMOS battery being dead or a bad memory module. (Because this board supports chipkill, you could have a bad module yet the system will boot still).
You don't see POST messages? Have you looked in the BIOS for POST messages stored? These could help point you somewhere.
If you're running out of options, could reset CMOS and see if it helps. Or at least helps show an error message.
Going further, I'd start pulling hardware one at a time until the beeping stops (PCI cards, storage, reduce RAM, and CPUs if there's more than 1 installed).
Oh, just thought of something; a bad/tired backup battery on a RAID card could do this too.
Does the beeping ever stop? And is it constant beeeeeeeep or beep, beep, beep... ?