Hello,
If I understand correctly, you create the ROIs on the anatomy template, save them as .mat files and try to load them in a subject.
This cannot work because the cortex meshes for the template and the subject are different, the vertices do not match point-to-point, and the scouts are simply lists of vertex indices.
If you have processed the subject MRI, you have access to an interpolation matrix with which you can project source maps or regions of interests (http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects).
When displaying the ROIs you designed, go to Surface tab, menu Scout > Project to > select the appropriate patient’s surface.
Cheers,
Francois