Here's something that has always worked for me. Give it a try, as it might work for you too. If mileage isn't added to your frequent flyer plan, either automatically when booked, or when you ask a ticket or gate agent for the courtesy, try writing a one paragraph letter, to the airlines' frequent traveler program, mentioning to them that on such and such a date, you flew on such and such a flight, and would they please apply the mileage. With the letter, and this is the key, include either the eticket, or a copy of it, or the boarding pass for the appropriate flight. I've never had them refuse that method, in fact I keep a few of these letters on my computer and just change the appropriate information, and send it off. Oh, and don't forget to include your frequent flyer number on the letter.
JJ