It could be. Looking at how to test the indexing for triples, you tighten the cable such that you don't get rubbing in the middle ring / large cog combo. I've seen a bit of rubbing going on in the middle ring / small cog combo a lot (it's my friend's favorite gear).

The chain is pretty slack at this point, though not as much as in small ring/small cog. I wonder if you're getting symptoms of a stiff link. What happens if you put it in the small ring/small cog (you may have to use some FD trim to keep the chain from grinding around on the FD). You could also just try trimming when in the middle ring / small cogs in case you do get some slight rubbing when the frame flexes.

I'm pretty perplexed, though.

If it's trying to autoshift in the small cogs, can you tell which direction? Does it try to jump up or down? You might want to recheck your upper limit.

The first place I'd look would be to see if there's a stiff or bent link or if your derailleur hangar is bent.