I hope my insights have you pointed in the right direction.
I've noticed that some browsers ALWAYS display them wrong, and others seem to get it right for some magnifications. Maybe lightbox is still working with the un-rotated image after it's actually been rotated into the new file? Or does its thing too soon, before it's rotated - and the thumbnail is generated after rotation? There are so many IF's in there that I'm not sure. Maybe more than 1 -auto-orient is needed?
It sure would be nice if there's an easy fix for ALL of us, even if it only works for future photos.

I can live with that. It will save me a lot of trouble.