I've programmed a dozen or so with zone 2 and not had the issue. The dealer I program for uses Yamaha amps. I know most of their amps have power commands for main off/on and all off/on. Perhaps the Zone 1 off/on is actually sending a all zone off/on. Perhaps you could test the original remote for this and learn the main or zone 1 power commands if applicable.

Another difference is my dealer asks that I leave all unused devices on always. It does speed up activities as all they do is input switching and we get very few calls. I use a separate activity for zone 2 that has just input selections and sometimes volume if it is variable not fixed.