I don't see any beep sound while booting my machine. Although my system has been working flawlessly since 2008 till date, I have every recently installed an application that gives a beep sound which I am unable to hear.
I guess the application is trying to use on-board motherboard speakers for this beep sound.
I have also updated the Realtek drives for my chipset but of no use.
Try to remove the memory modules and boot the system.
If the onboard speaker issues three beeps, then you know that there is nothing wrong with it.
Refer to the TPS for more information:
All the best,