Alignment between a segmentation volume that contains just parcellations and an FA volume directly is not something anyone would recommend, I think. Instead, you can use a T1 or T2 weighted image for your alignment. The warning messages here are just warnings to make sure you are aware you are dealing with oblique datasets and should do something like alignment or another warping transformation to handle the differences in obliquity. Still just running an alignment command does not guarantee alignment. Try using a different dataset for your alignment, and apply the same transformation to the parcellation using "3dAllineate -final NN -1Dmatrix_apply ..."