Relevant Dresden Codak: http://dresdencodak.com/2009/09/22/caveman-science-fiction/
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"Hey look, Homer's got one of those robot cars."
"...One of those American robot cars."
...let me assure you that it is an often congenital condition that causes the eyes to be misaligned. The causal effect doesn't work in the opposite direction: misaligning your eyes does not cause strabismus. The only way to cause strabismus without it being a congenital condition is via nerve lesions, and when it develops after early childhood it usually causes double vision, not amblyopia (which is what this article is describing).
Not to mention that while watching a 3D movie, your eyes are fixating on the same point in space, just seeing different images of it--the 3D effect wouldn't work otherwise.
Not to mention that even if strabismus could be caused by intentionally mis-aligning the eyes (a sort of "don't make a face or it will stick that way"), and 3D movies misaligned the eyes, I can't imagine doing it for a couple hours at a time every few weeks would be a huge deal.
Here's why: I know that when companies over-reach, then it'll be me who's pulling the late nights and weekends to deliver, not the guy that over-sold the product.
I'm 26 and already experiencing this joy.
By watching you pay at a convenience store (as an example). When somebody's wallet has a lot of cash in it, it shows.