I have had the same problem. Just to make sure both pins got used at Bethpage Black in our 4 round tournament, I set them to be different in each of the 4 rounds. Still, the first 3 rounds all had the same pin placement on 15 (not sure about round 4 yet). I have noticed this problem ever since I started creating tournaments. I just assumed it has never worked properly. On several courses I have set the pins to be either hard or easy, and when the tournament got published, it was the opposite of what I had tried to set.
I wish they would not only fix the issue, but make it more specific, like "pin placement 1" or "pin placement 2". It would be nice if we could adjust it for each hole, like we can for tees.
BP