I've tracked down the problem. I'm not sure why this one hasn't surfaced before. The problem is located in the function 'self.determine_param_set_type()' in the file 'specific_fns/model_free.py'. The lines
# Skip unselected residues. if not self.relax.data.res[self.run][i].select: continue
should be commented out. This was identified as a bug ~20 lines below and was commented out there! I'll fix and commit the bug tomorrow when I have SVN access.
Edward