USB Issue
Something to try for troubleshooting would be to disconnect everything but the mouse and the keyboard. If the problem goes away after doing that then at least you will know the keyboard and the mouse are not the problem. From there, I would suggest that maybe hook one item at a time to see which one of the devices causes the set/reset beep that indicates there is a problem.
I had the exact same issue with my pc and thru the process of elimination I figured out the problem was my HP printer so I disconnected the printer but the problem did not go away. Turns out that I had to completely remove anything remotely connected with HP to fix the problem where it finally went away. HP puts crap all over the printer and I had to hunt down all the HP folders and files and delete them to finally get rid of the noise. I will never buy another HP printer to say the least.
Just using the process of elimination should help you find the USB device that is causing the issue.
Take care and good luck.

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