I see... so that makes sense that I could have gotten jerachi without a PGT file and only with PCD. It also makes sense what @Ammako I must have gotten Dragonite, which came with both PGT and PCD, then Jerachi distribution only came with PCD, so it overwrote Dragonite's PCD but since there was no PGT then Dragonite's PGT remained. Weird...
As a side note, I merged latest commit but in title it still says (20161231) so makes it hard to determine if Im actually running the latest commit. Any way to check?