just to update here also, here is my workaround. Again Sony STR-AZ3000ES. Device buttons work fine, but activities wouldn't power or change input on the Sony. After much testing, I increased the powertoggle command tp .5 seconds through the device power settings. This made the receiver turn on and off.
To make the input work correctly, I made the harmony learn a new command, naming it something simple. Then customizing the activity, i can add the new command (there was a basic set of commands there initially, but oddly no input commands?). Adding the new commands lets it power on, switch input.
funny enough Help won't fix the input issue when used. Help must only run through the mandatory activity sequences not the added in buttons.