Many of us ride asymmetrically, which was the subject of a thread a while back. All of my leather saddles (6, so far) show that I sit deeper on the right. Some saddles move more than others. When I feel under both sides of the slotted Selle An-Atomica as I ride, my right sitbone is about 5mm lower than the left.

But if that asymmetry is causing pain, that doesn't sound typical.

Have you tried rotating the saddle+seatpost one way or the other?