I found the cause.
Since our anatomicals are not of the whole brain, but only the sections inplane with the functionals, the rotations/translations that 3dTagalign made cut into useful brain areas for us. This may not be an issue when this is applied to a whole brain.
When all the tags were set in one slice, nothing was cut off. We can do this untill we get our functionals aligned with the high resolution whole brain anatomicals.
Thanks