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This was an opencv library version conflict, as I suspected. I had opencv 3.4 also in a development folder. Despite camera_calibration being built with the opencv 3.3 that came with ROS kinetic installation for some reason ldd showed a dependency to a lib in opencv 3.4. I think this dependency came through a thirdparty library built with opencv 3.4 and installed in the system. Interestingly enough other opencv calls in camera_calibration worked well but only showed the problem when opening a window.
I uninstalled opencv 3.4 and rebuild a bunch of libraries with ROS's opencv 3.3 and it worked.
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