Maybe some of your images are rotated 90 degrees for some reason? That would result in a combined image that was square. Unlike dedicated astro cameras, DSLRs will detect the orientation of the camera when taking the images and it will adjust the orientation of the generated image accordingly.
Also, someone recommended to me that I *not* use a superbias. So I did a comparison of a master bias vs. a superbias, and he was correct - I much prefer the plain master bias. I took 100 bias frames in my test.