Hi Wayne,
Hard to tell what is going on but I suspect the dataset are way off compared to the template. For example, if datasets are quite oblique you can specify an initial transform to deoblique them first. Read @auto_tlrc's help for option -init_xform and see if suggestions made there help you get better results.
Otherwise, upload a sample dataset and I will try to look into what is causing the alignment to fail.
cheers,
z