One thing you can try is to force one of the Yamahas to pass the full TV EDID, rather than the modifed one that the Yamahas normally produce. In the back of my mind I remember an append from 1-2 months ago in this forum that explained how to (or led you to what to look for in the directions). You might try to do that with one of the Yamahas and see if that has an effect. That would at least provide a clue as to where the problem is located.
Use the "Search this forum" function and search for "Yamaha" (no quotes).
Unfortunately, that isn't a good long term solution since I think that would likely result in stereo output for one of the Yamahas. As Colm said, the source determines the formats. It does this based on what the sink destination devices report they can handle. Since HDMI can only have one video and one audio stream at a given time, the protocol attempts to only output something that would be compatible with everything connected (even if the device is off, usually).