Sorry if I was not clear enough.
If you have a 1x1 square dielectric and you offset it to (5,5) as per your example:
D square.txt 1.0 3.5 5.0 5.0 xref yref
for (xref, yref) to lie within the square you must specify it as e.g. (5.5, 5.5).
This is what I meant saying that the reference point is not translated / offset.
Hope now is clear!
Cheers,
Enrico