There is a lesson here - never, but never let go of your original boarding passes or tickets. When they're gone they're gone, as I learned to my chagrin with KLM. They subsequently lost my business as they enforced the rules to the letter of the law, rather than thanking me for 50K worth of business.

That said, I imagine (hope) that DC would have checked each individual ticket for valid fare classes. Three weeks is a long time, but DC can be very slow sometime. I'd wait a week or two more before worrying unduly. If you have the details of the bmi flights, it shouldn't be too hard for them to find you on the system and allocate you the points. The *A partners might be a bit more difficult. If UA is among them, ask them for a receipt for the tickets, or get your TA to give you some documentation.