That's a crazy one...
Sorry I have no suggestions, but I want to try auto punch when next I am in my studio and I'm curious whether I can reproduce this.
Just to confirm:
1) It really does get progressively worse? It's not just a fixed offset? (48k/44k1 = 1.09, roughly 10% slip)
2) Everything was recorded with the same setup? Or were some tracks delivered from another studio?