My history matches undersky. I have never not received credit for a UA flight (knock on wood). I have had some trouble getting US credits when irrops occurred (2 different flights), but a phone call or fax fixed them both.
Here are some things in the future you might try to reduce your risk:
1. Check in online. Print the boarding passes to a PDF or TIFF (use any free PDF creator programs or Microsoft XPS Document Writer in the printer choices) file and save it. That way, you can always print out your boarding passes later if needed. Of course, this only works if you don't change your flights during the trip. This also gives you a record of your ticket number, which you can use for the online credit request if necessary.
2. Enter your MP number into the reservation when you first make it. If you use .bomb to make the reservation, login to your account first then make it. If making a reservation on a partner and their website won't let you enter a UA MP number, call them asap after making the reservation and add it.
3. If you check bags, give the agent your MP card and ask them to triple-check that your MP number is on the ticket. You should know that it is from the online check-in BPs, but it never hurts to check. You can also ask at the gate.
The above especially hold for *A partner flights, especially US.
Sorry to here about your experiences, but I hope this helps you in the future.