For reference, I think the issue had to do with the orientation of these two subjects. I added tome code to use 3dwarp -deoblique to the dwi_orig.nii.gz and then ran orientLAS and it worked this time.
The only thing I am unsure about is if this will nulify the bvals and bvecs I have and ruin later preprocessing steps? This is the only solution to the problem I have found thus far though.