Hi Rocco,
unfortunately I'm afraid we have not addressed this issue. What I usually do is re-run with different options to 3dAllineate, such as -cmass or adjust the mask (if there is a glaring masking error) and re-run.  We could add a flag that allows for additional options in the next release, but in the meantime, you have to edit manually to use these options on a one-time basis if the mask isn't incorrect. For example to add the -cmass option, edit line 322 from:

3dAllineate -automask -prefix ./$epi_mask.crg2mni.nii -source $epi_mask+orig -base $PESTICA_DIR/meanepi_mni.nii -1Dmatrix_save $epi_mask.coreg.mni.1D


to:

3dAllineate -cmass -automask -prefix ./$epi_mask.crg2mni.nii -source $epi_mask+orig -base $PESTICA_DIR/meanepi_mni.nii -1Dmatrix_save $epi_mask.coreg.mni.1D

And edit similarly for other options. Unfortunately I don't have a good guide as to what works, but for large offsets, this sometimes works.
Erik