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I have had the same problem, also working with ultra-wide angle lenses. It seems the problem is the StereoRectify function which may calculate some invalid inner and outer rectangles as a basis for centering and scaling the rectified images. I think the reason for this is that it tries to undistort the extreme boundaries of the original image, and this does not always go well, especially in the corners of images when you have a lot of radial distortion. My solution to the problem has been to rewrite StereoRectify so that it only calculates the inner rectangle and only on the basis of four points on the image borders: North, south, east and west. That way I get a stable behaviour. The price to pay is that the free scaling parameter alpha will not work as specified, but for my purposes it is enough to perform some scaling relative to the inner rectangle.