...I know you measured your chain stretch at <.75 (you said so), but this sounds like exactly what would happen if the chain and that cog were a little worn.
i.e., the chain and cog are worn just enough that the new missing link, which is not worn, is catching and skipping a little because it's a bit off from the rest.

I think that if it were me, I'd try a new chain and cogset, and see if that fixed the problem, or at least remeasure the chain stretch using a different method like a straight edge.