Thanks so much for taking the time to post that video. It really does help to get a listen for myself.
It does sound like a motherboard/system beep. To be sure it's a motherboard/system beep, you could try putting in headphones. If you hear the beep coming out of the headphones, it is being generated within Windows. If it still seems to come from the computer itself, then it is a motherboard/system beep. Those type of beeps usually occur when the battery is low or has reached full capacity (on some units), and also when a key is being held down.
Do you ever experience the beep when the computer is turning on, before it gets to Windows?
Have you noticed if the same program is running when you experience the beep?