Of over 100 segments flown on CO metals since NW-CO announced their partnership, I've never had to call in for miles not posting to my NW account. Not once.
I'm not sure why you're having this problem.

Anyway, you mentioned CO codeshare. What flight metal are you talking about?

Related to your flight on CO this month, I remember my brother had a problem with a missing flight segment posting to his NW account last year. I called in to WorldPerks on his behalf. IIRC, I gave them his CO e-ticket number and no boarding stub is required at all for the miles to be adjusted on his account.
Perhaps you should call in and see if they can post the miles for you by supplying just the e-ticket number.