That would make sense as you are using your eye muscles in a different manner to view 3D then you normally do when you view the world. You can strengthen those eye muscles by watching more 3D as long as you don't have a vision impairment or eye muscle imbalance to begin with. Such ailments are what cause the symptoms such as headaches, dizziness, vertigo, etc.
I got a minor headache the first time I sat through a feature length movie with my active shutter glasses. The next time my head felt a bit "fuzzy". Now, I don't experience any issues at all, even after watching for like 4 hours. Your explanation seems rational and makes sense.
When your buddy comes over and complains about eye strain, just say, "Dude, you're a girly man. You need to workout...your eyes!"
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