No worries, but that's a tough one! DSI studio uses image space and doesn't use the same coordinate space as mricron, and DSI studio doesn't apply any shifts. But you could try changing the hdr.image_orientation_patient field in the trk header to [1 0 0 0 1 0] or [-1 0 0 0 -1 0], for LPS and RAS, respectively, if they seem to be flipped. It's more likely that there's just a shift off somewhere though, like you said.

I was looking over the scripts that I adapted from the Vista lab, and there's a point after it converts to MNI when it also applies a qto_ijk transformation from the template image which is just a shift from the template header, and it's not clear to me why this is being applied. I would suggest removing this qto_ijk transformation, but it's hard to say for sure without sitting down and playing with it. 

I'm less sure about the FA map being off in mricron. You can reset this in spm though. In matlab run spm, then click fmri, display, and then use their gui to reorient. This may fix the mricron issue but I'm still suspicious about the DSI studio one. If you do this, sometimes you have to manually reset the hdr.private.mat0 field in the nifti header before normalization :(

What you're doing should work though. Is there a way to verify the tracts in MNI space?