hi,
the problem is that if you set a periodic boundary condition is that you are repeating this defect throughout the whole crystal. However, if you placed your boundaries a little far from the defect, then the repeated defects won't significantly interact with each other and thus you will get the same response as the one with a single defect. You can check this by drawing the field distribution for the defect mode and if it was small enough at the boundaries then this should be correct.
For setting it up, I would just place the periodic boundary 3 cells away from the defect and check the field. if it is small near the edges, then you are done, if not then you will need to place your boundary a little farther,
hope this will help,
Adel