I had exactly the same situation on a NW codeshare (CO metal) from EWR to DTW. Told by the agents at AS twice that the flight number was the important thing for status miles. Credited as CO rather than NW mileage.

As a result I was 92 miles short of 55K and missed a 10,000 threshhold bonus. I have complained in writing - I'll let you know the response - if any.

They should be consistent with their policy.