Did anything ever come of this? I have also been getting this behavior recently (in those same conditions) but I am running racing cats and downpipes. Interesting to see it also happens stock at times.
I am experiencing this same issue - and I've completed your diagnosis and more. Only difference is that I'm currently running an MPT 93 PRX tune. Despite that, I've had this tune installed for months now - and this behavior is new.
Did it ever return after your tune was installed? Or all good...