This recently happened to me for a DOH-CGK leg. First step would be to repeat the online claim, BA have admitted there is a bug in the system to me. My next step was a call to the Silver Line which was no help. I approached Qatar direct as recommended by BA and they said it was a BA issue as my FF Number was clearly on my boarding pass. I then submitted a formal complaint through the system attaching my Boarding Pass and the e-mail from Qatar. Because I was still not getting a reply I used the BA twitter feed by private messaging them. They were helpful but still had to follow up a second time. Points eventually posted but two months later and not sure of was the complaint or the twitter follow up that actually resolved it.