Thanks for the suggestion. Unfortunately it appears to be a combination of items - not just equipment or just cabling. It works fine across HDBaseT / Matrix direct to the TV. Works fine for other sources through HDBaseT/Matrix/Receiver/TV and works fine local to receiver/TV.
I have swapped all of the HDMI cables on both ends of the HDBaseT connection and the connections to the switch. I have tried a seperate HDBaseT receiver and inserting an HDMI repeater in case there is just a limit in the number of hops for stable signal.
My last items will be trying a different HDBaseT sender and a seperate cat5 run between HDBaseT units. Other than that, I'll try a different AppleTV unit since all my other sources (DirectTV, Windows Media Center, Security Camera DVR, Control 4 Onscreen GUI, etc.) all work with this same configuration and cabling.