Welcome to the forum!
To help us narrow down the issue, I have a question. Not to be insulting, but have you followed the steps on page 132 of the owner's manual under the section, "Selecting the input source of Zone 2 or Zone 3"? I ask because on page 131 where it discusses selecting Zone 2 there's the wording, "Controls the Zone 2 amplifier or tuner functions." So, it makes me think that it's possible that you just haven't done all of the steps necessary to select a source other than the tuner.
Let us know and we might be able to help you track down the issue.