OK,

I believe I have been doing as you say. And you are correct, my USB and ALPC configs differ in the External LED settings.

For HiFi on the USB I have External LED Mode set to Dim with Control Set brightness on 2. I have the Status LED brightness on 1/or off. (I only want to see it during an alert, the control set LED on 2 is enough for me to let me know its on and its status).
OK this works fine.

I remove the USB, fire up ALPC, in Modify I set the External LED to Dim on 2 and slide the Control set slider to 1/off (and wonder why is there a control set setting in ALPC? Its firmware disabled anyway.) I save on line and then download.
It works fine.

Now I kill ALPC and when she switches to HiFi my External LED is on. No longer do I have the control set LED only.

I had it the way I wanted it until the new FW I downloaded to install my TX's.