Different things, may be an incompatible processor or memory.
There is a very good resource available at http://www.intel.com/support/motherboards/server/sb/CS-029657.htm to troubleshoot such issues. Also, look at the compatibility page for information on what processor, memory & peripherals you can use.
You mean the system only starts beeping after the OS loads? I don't think the board generates beeps after POST.
Do you have a RAID card installed on your system? Some RAID cards may generate beeps as well.
Thanks Edward. I already was able to diagnosed the problem. You are correct when you mentioned about the RAID thing. I accessed the Raid Bios and rebuilt a disk. After that the beep stopped.