That's how it works...when an active transmission is in progress, the amp is on...as it should be so you can hear it. When their's no transmissions, you can set the timer as to when the amp goes off to alleviate the "hum" or "scanner noise". I have mine set also at 100 milliseconds but never had an issue with loud humming. Maybe someone here who has uploaded the firmware and installed the part can tell everyone here if it's completely eliminated.
I installed the part and the firmware and you can still hear the hum when the frequency opens up until the close of it slightly. It's still a bit noticeable.