Charlie,
How you transform your FA to T1 space may (or may not) be the problem here. In my experience, the calculation of this transform can be the hardest when trying to get from a standard space to FA space. I have found some success by calculating a B0 to T1 transform using the FSL epi_reg function. It's definitely not made for this type of transform but, I've found it to work better that FLIRT of FNIRT for a T1 to DTI space transform. Alternatively, sometimes when my transformations are as far off as yours are it's because I either missed an affine transformation step, doubled-up on a transform, or applied the wrong transform. Without seeing the code from start to finish I can't rule-out any of those possibilities. Good luck in finding your solution!
-Bryson
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