I glad you got your sound issue sorted out. Here's short video of mine with both the original terrible whistle and the upgraded whistle Lionel offered us when it came out.
I don't run mine with a battery and it doesn't cut out going over any Fastrack turnouts including the O72 ones. At this point, if sound is dropping out, you must be your Atlas turnouts like the curved O54 or some of the number turnouts.
There was some discussions on mods you an do to the turnouts to improve this if you search for them or ask others with the problem.
Another option is to put a 9 volt battery in the tender or a BCR with a charging kit in the tender and that would solve the problem as well. Personally, I would go with the BCR option and never worry about opening the tender in my lifetime.
