I had an issue with the beeping as well!
I read it beeps when it thinks it runs the pumps too long.
What I did to fix it was reset it when the ATO needed to run for awhile. When it runs the first time after a reset, it records how long it runs the pump for. if, on subsequent runs, it runs the pump for a little longer, it thinks something is wrong and starts beeping.
So, just reset yours when you need a big fill and it'll stop the unnecessary beeping; and give you piece of mind that it wont flood your house if its sensor malfunctions.