I had this happen to me once. Flying home BCN-IAD-PDX and went for a buy-up option and was definite that it was both legs. When I checked the new itinerary only the international portion was upgraded to J, and the IAD-PDX remained in economy. I didn't bother to complain because I was skipping that leg and flying IAD-PDX on a separate one way ticket the next day, which incidentally was already booked for domestic first.