Hi Jessica -
If the external program (e.g. matlab) is ignoring the transformmatrix field of the metaheader then what you are seeing is expected behavior for the harden step.
Instead of Resample Scalar Volume, which only changes the pixel data, you can use Resample Image (BRAINS) which allows you to set the input image, the transform, and a reference image that defines the output pixel grid that you want. Then the pixel matrix should work in matlab.
Hope that helps,
Steve