Yeah, my story is the same as the OP:

Plat wife and I flew LAX-JFK-AMS-BIO in May and returning BIO-CDG-LAX with a combination of DL and KL on the outbound and all AF on the return June 3.

The check-in agent at BIO on the return said our Skymiles number was "wrong", she could not correct it, and I'd have to file for missing miles with Delta. This is a Delta-purchased rt ticket with a 006 number.

Two weeks later, only the outbound LAX-JFK and AMS-BIO segment post.
Wife and I both write in on the missing miles link on the flight history detail page on Delta.com

She gets an e-mail in three days confirming all her missing miles are restored. I get a curt e-mail saying "Please wait two months for partner flights to post."

So I write in again using the same link just over a month past my return flight. Delta credits missing JFK-AMS segment flown on KL on the outbound, and I get the EXACT same "Give your Skymiles number to the check-in agent" as the OP. Which I did. E-mail gives no indication of whether my return will post. On BOTH e-mails, I included scans of my boarding passes, which have my Skymiles number on them.

I'll wait another month and file for missing miles again. I think this is more a case of stunning incompetence than evil intent. Skymiles aren't really worth enough to think of elaborate schemes to cheat us on them. I think.