I was debugging and moved to an audio only source. Interestingly, sound works OK, so it appears to be related to the HDMI audio source. So I unplugged all the HDMI inputs and ran my Harmony sequence as normal. It switched to the correct input.

So there's something definitely related to the HDMI input. Next, I'll have to add each HDMI input individually to see if can narrow it down the particular one. Hopefully it's a cable or even just one of the HDMI inputs going bad. I can live with that vs having to repair/replace the AVR.