Two things for you:

I've not had trouble with Pio plasmas, and did one yesterday. However, I never have the input command that close in time to the power on. Typical for me is:

Select input on TV
Power on TV
Power on Audio
Play disc (if applicable)
3 sec delay
Select audio in
Select audio surround mode
3 sec min delay, up to 6 or more sec for some displays
Select input on TV
Go to device page

I like select TV input at top as well as the bottom when the monitor is already on. It quickly switches to the right input so there is no several second delay between the switching of the sound and pic.

Regarding your Yamaha surround problem: I solve that by first switching to a useless surround mode, 1 second delay, then back to the one I want.

Say you want all channel stereo. Like you say, push that button a few times and you are all messed up since they rotate from one to the next. If you are already in the all chan stereo mode, switch to hall or stereo or some other mode, delay, then back to the all channel button. Providing the client does not manually mess with the surr modes, you should be able to come back to it every time.