I ran into this a couple of years ago. I was supposed to fly from Singapore to Seattle with a stop in Tokyo on Northwest. It seems that even though my flight had the same flight number from SIN to SEA, a different aircraft was to fly the sector from NRT to SEA, and I missed it due to the SIN to NRT sector being late. Northwest had me rebooked on United from NRT to SFO to SEA. I asked Northwest if I would still get Northwest frequent flier miles, since it was my intent to fly Northwest, and it was not my choice to fly United. I told them I was counting on these miles because I had planned on using them for a free trip on Northwest from RIC to ANC, and without them I couldn't make that trip. Northwest told me no, that they wouldn't award me miles for a segment I hadn't flown, no matter what the reason. They said that I would get United miles, if I belonged to United's program.
A couple of months later, I got my mileage statements from Northwest and United. Even though Northwest had told me otherwise, they had credited me with full mileage from Singapore to Seattle, even though I had only flown with them from Singapore to Tokyo. And United had credited me with mileage from San Francisco to Seattle. They didn't give me credit from Tokyo to San Francisco. I sent them my boarding pass, but they wouldn't accept it as proof that I had made the flight. They said I also needed to send them the passenger receipt of my ticket. Since I never had a United ticket, I couldn't do that, so I let it drop. I figured I had received more than I was entitled to anyway. I had full Northwest mileage plus partial United mileage. But why did Northwest's agents tell me I wouldn't receive Northwest mileage when I did receive it? Don't they know how their own program works?
Fly Eastern's Golden Falcon DC-7B