Try to randomize the trainer data multiple times by clicking the "Trainer" button to open, randomizing it, closing the "Trainer" window and repeating a few times until you see that trainers actually randomized. I also had this problem, and to fix it, I just randomized multiple timesUsing SaltySD and PK3DS randomizes the the wild encounters ans starters but not the trainers I put the "4,5,6" GARCs in the right place after using the 'randomize all' option and closing PK3DS.