Actually, eyeglasses are not the same; they refocus light into your eye, and you actually see through them, so the eyes still converge and focus on the same point in space like they’re supposed to. A VR or 3-D film experience forces your eyes to focus on a fixed point in space (the screen) but to falsely converge at another point in space in order to make out the three-dimensional image and its corresponding depth.
Additionally, one person’s experience does not make science. There are numerous anecodotal complaints of patients who get headaches from watching 3-D films and VR for lengthy periods. It’s one thing to watch a 90-minute film, but to be playing a game for more than a couple of hours hours with a 3-D viewer where the eyes must converge multiple times per minute, if not second, is another matter.