I noticed this after updating to the newest (v3.03) firmware. I had to rebuild the codeplug after an error so this must have been enabled by default in a newer version.
Open the optional settings window then the Alert Tone tab.
Common Setting > Optional Setting
Change the frequency from 1000hz to 0
You’ll still get a single beep when pressing PTT after this.
Change Talk Permit to Analog or Off to disable the other beep.
Hope this helps. It was driving me nuts.
73 de KF0IZW