Ok, I am using the G98 video switching now but when I was using the G68XXV, each source has individual Copy/Zone 2/3 settings. In particular, Use Main Inputs should be set to Y. (Default = Last Valid). Check these with Mconfig. You can set every conceivable option on these. There was a Zone function upgrade in one of the firmware changes so check you have the latest versions.

You are correct that on the front panel Copy = Source is the correct setting.

Malcolm