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If you are getting the same effect on your images using the "official" OpenCV sample calibration program, then the problem is likely in your images.
The first thing that comes to my mind is: What kind of stereo camera rig are you using? Is it a commercial stereo camera or is it custom made? For best results the left and right cameras should be as parallel as possible. Otherwise you can get wildly undistorted images depending on how much overlapping area there is between left and right cameras.
Second: how many images are you using for calibration? For best results you should use images with the calibration pattern in as many different positions and orientations as possible.
Maybe if you post some example images we could be more helpful.
