Yes, it is a custom built. PSU is Corsair 650W. I'll test with a spare and see how it goes.

@snowbunzz
Like I said, I'm pretty sure it's not the POST beep that is the "beeping" that I am referring to that is happening. The beeping happens after the POST, while Windows is loading. The beep is much like the beep that indicates the computer is overheating, but the computer starts fine and runs without any trouble.


Updated original post with more information.