I would assume that for hundreds of years, perhaps longer, the third Sunday of Easter (second Sunday after Easter) was Good Shepherd Sunday and, for those Lutherans using the one year lectionary, it still is. Even in Rome there is this disconnect. Since the three year series has moved Good Shepherd Sunday to the fourth Sunday of Easter (third Sunday after Easter). I had been curious to find out why this move took place but had never bothered to research it. Now there is an answer of sorts.
Since the three year lectionary was invented by Rome (and everyone else followed, for good or for ill), it was in Rome that the answer, of sorts, is to be found. It seems that there was much debate over this when the calendar was being reformed. In the end, the decision was made to keep Good Shepherd Sunday on the Sunday it had always been. But then, you might ask, how did we end up with the Sunday moved one week later in the three year calendar?
In July of 1966 the situation was thus:
The apparitions of the risen Christ must occupy the principal place. Currently they are read on Easter Sunday, the six days of Easter week, and on Low Sunday. Two possibilities may be considered here. The first proposal is that the six Gospel readings in Easter week be kept in their traditional locations.
The alternative proposal is that these same Gospels be read on Easter Sunday (Mark, Luke, John) and the 1st Sunday after Easter/2nd Sunday of Easter (the other three readings from John). The pericope of the Good Shepherd then ought to be transferred from the 2nd Sunday after Easter to the 3rd Sunday after Easter/4th Sunday of Easter...But in the end, the alternative was dismissed. So the proposal accepted by the Fathers of the Consilium was that Good Shepherd Sunday should remain in its traditional location, as the 3rd Sunday of Easter (2nd Sunday after Easter). In July 1967, the proposal distributed to every episcopal conference, the participants of the first Synod of Bishops, and around 800 periti (biblical scholars, liturgists, pastors, etc.), that Good Shepherd Sunday is in its traditional location. However, two years later, when the typical edition of the Ordo lectionum Missae was promulgated in 1969, Good Shepherd Sunday ended up having been moved to the 4th Sunday of Easter, with the accounts of Our Lord’s appearances to the disciples at Emmaus (Years A and B) and at the Sea of Tiberius (Year C) read on the 3rd Sunday of Easter.
Concerning this dual proposition, the opinions in the Coetus and among the relators were diverse. The second proposal has the advantage that the different accounts of the apparitions are read on Sundays and would, therefore, be made known to the people, which currently does not happen; the disadvantage is that, in this way, the same pericope is not always read on Easter Sunday, and that the Gospel of the Good Shepherd, as well as Good Shepherd Sunday, must be transferred to the week following, which does not please several [members].
Why? According to Annibale Bugnini, it was thought that the Good Shepherd them interrupted the sequence of resurrection appearances and so the 1967 Ordo was “radically revised” in early 1968 on the basis of 460 responses received from the Bishops and periti who were given a copy. So, apparently the concilium charged with the reform came to one conclusion and, after how many responses we do not know, the decision was made to change the lectionary. Of course, that sheds so much light on the matter. What is does reveal is that at the time so many things were in a state of flux and the changes were coming so fast that they were accepted almost without thought and so we ended up with the one year and three year lectionaries out of sync in Lutheranism and in Rome and it has, apparently, been going on too long now to do anything about it.
Read it all here: A. Bugnini, The Reform of the Liturgy 1948-1975 (Collegeville, MN: Liturgical Press, 1990). For if ever there was someone who was making things happen, it was Annibale Bugnini and, it seems, even Paul VI did not know what was going on in the reforms that have become his convoluted legacy. And that is, perhaps, the only real reason we have for why the choice of the larger group was overruled and Good Shepherd Sunday in the three year lectionary ended up on a different Sunday than the one year lectionary.