I think the ratings are working as we would hope; those playing one course (with OB) have ratings set as a group while those playing a different course (without OB) are set as seperate group. It's just a odd combination of overall poor play by the the AM propogators (or excellent overall play by the Open propogators) in the 3rd round that have allowed them to have a higher rating at the same score while on a easier course (I'm calling it a seperate course due to having different OB rules).
This is dead on. Different OBs = different course. There's no adjustment necessary (or possible) since the ratings were calculated as two distinct courses already. The math is what the math is.