I looked at that so many times and never noticed that. So I guess I have 2 choices:
1) Stick the Alaska segments on Cathay's asia miles (which may not be easy to do)
2) Book the Alaska segments not as codeshares so I get AA credit for them.

Where I was confused is that normally you would get AA miles from Alaska even though they are not in the (or any) alliance.

As an aside, I would have thought the desk would have pointed this out to me but they always just resubmit them.