The AT Pro will make a noise as you use Auto Ground Balance. It is when the tone is at it's lowest volume that the machine is balanced. I think it is on page 31 in the manual.
I know what your talking about mine dose the same thing, so I will ground balances it on shore where I am hunting , seems to work fine doing it that way. I have read about this before on here a while back , where some people were having the same problem!
Flakefinder thanks for your response. I do the same as you do and it works fine in the water after so maybe I'll just keep doing that also. AT pro is a great machine.