For Option 1: There are no external speakers attached to the system so there is no "odd software" installed to cause the issue. As for the possibility of Malware or a Virus, all of our systems virus and malware tables are up to date and they detect nothing out of the ordinary.
For Option 2: The beep is coming from the computer itself. I have done a deep scan analysis of the hardware and everything there is working fine. So far I have found nothing in BIOS that could be causing the issue but I am still looking.
I am certain it is not a UPS or surge protector. There is no UPS on this particular computer and the surge protector has no auditory indicators.