The settings to uncheck it in the general configurations don't seem to always hold. A week goes by and I find it checked again. when I enable Minerlink it also gets checked again. Turning minerlink on also doesn't hold.
where is the beeper on the S5. Bitmain maybe needs to look into another way to disable this beeper.
The beeper signifies no pool and / or internet connection, ie its not mining. You are correct that certain actions in the software will retick the box, and sometimes the setting won't stick at all.
I don't have a good picture of it, so you'll have to look from here. Its hiding under the BBB towards on fan side of the controller, and the opposite side to the fan cable. Its a black cylinder. If you screw one of the side panel screws into it it will silence and / or destroy the beeper.