I have the same issue with mine. No firmware version since getting it and no app version going back to 1.6 has made the beep setting in SimAppPro actually work and turn that beep off. I've tried different cables and different USB ports.
I've read the manual(s) on WW's website as well as the one near the top of this forum, and none of the relevant manuals seem to even mention the beep setting. If you have an idea what manual this might be in, I'd be happy to concede that I didn't read that manual.