Regardless of trauma-induced suckouts, people each hacve their own response "signaure", as all ears are NOT created equal.
Paul, the aural height information is a function of your pinna, NOT the musical software. It's true that stereo reproduction won't often provide visual soundstage cues, but your pinna certainly help tell you whether you're sitting in the balcony or on the floor, for example.
With headphones there's no vertical cueing.
I too forgot this aspect of our hearing apparatus a few weeks back when out at Symphony with my acoustician-guru and friend Tom Horrall, who responded with a "What'd you do, cut off your pinna?" after a comment I made about not being able to locate a an extraneous noise source up near the ceiling. I won't forget again!