Well I cant be sure why it's hard to focus on if I cant see an image however anim8or doesn't actually do stereo imaging; I mean you can do it manually but not automatically. So everything is up to really.
Somethings that may be the issue is because the depth you have created (the difference between the distance of the camera in the two renderings) could be much to great. Another thing could be the images themselves being displayed too far apart causing the viewer to have to go slightly cross-eyed in order to see both images as one (the two images on screen are too far apart).
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