I have some suspicion you are correct, but figured I'd try it and see if it fixed it (the breadboard layer missing entirely is the fault I know of and that isn't the case here). Your fpz file has a full 14 pins defined (I think) which are not in the svgs which usually causes problems and schematic (which I hadn't looked at before) is odd (it has an oddly named active pin on the top left labeled 0.11 in in a square and is missing the relay contacts although the pins for them are present and appear active). I'll continue poking and see if I can do anything. Perhaps some of our better parts makers will have some suggestions as well.
Peter