Well spotted. I have created a github issue to describe this behavior and my solution:
  https://github.com/rordenlab/dcm2niix/is...
Please test my solution, it simply negates the shear. I suspect there are more complex but generalized matrix multiplication solutions, but they are somewhat complicated by anisotropic voxels. For this reason, I hope my simple solution proves robust. Coming from MR, I have very little exposure to CT exemplars, so please validate my solution.