I just booked a Z fare on .bomb and saw the same message: "This itinerary includes one or more flights that are ineligible to earn mileage or Premier qualifying credit." I called in to check, and the CSR reconfirmed I'd get RDM, PQM, and PQD on the flight. She said this message has "always" been there since they converted how they calculate PQM earlier in the year. That seemed fishy, but I'm glad to hear I'm not the only one seeing it on recent bookings.

If it were true I'd immediately cancel (I'm still within 24 hours) and book the same trip on Etihad, which is the same price for the trip albeit 8 hours longer flying. The only thing that has me sticking to United is the 30,000 PQM I'll get for IAD-LAX-MEL and back.