One of the beeps indicates successful POST, and the other beeps are generaged after initializing each USB device. I suppose you have a USB keyboard and a USB mouse installed, plus two built in virtual USB deviced for remote KVM, you'll get four beeps. It's expected. See http://www.intel.com/support/motherboards/server/sb/CS-031822.htm
Very good information.
I unplugged the USB mouse and keyboard and I get three beeps now. From your description, this is the emulated mouse/keyboard, then successful POST beep, correct?
Thanks for the help! Now we can get 2008 R2 in place with a bit more piece of mind.
Yes you're correct.