So was the solution just to replace your audio interface with a newer, shinier, fancier one?
I’ve had the exact same issue with my setup.
Software: Cubase LE Elements 8
Audio Interface: Digidesign MBox (generation 1, I know, I know)
Driver: Asio4All 2.14
Exact same issue - a regular beeping sound chimes every fifteen seconds or so, only when an audio input has been added, and only when the USB interface is in use. It almost sounds like one of those trial programs that lets you use in in “demo” mode in exchange for messing with the audio a few times a minute, only in this case there’s no reason for it to do so.
It’s absolutely bizarre. I’d love to see if anybody found a way to solve this issue, I know my interface is old, but it still works perfectly fine with ProTools and even Garageband, I kind of don’t feel like spending hundreds just for Cubase compatibility.