Last week on nrt-ord flight, my name was not on the manifest and I was on C. The flight attendant asked to see my boarding pass (which was issued by jAL as my first segment was on jAL. She later apologized and said one other girl was also not on their manifest but I didn't ask what cabin she was in. I got my miles so I was scanned and in the system.
She said she has seen people not in the manifest but was surprised they had 2 out of NRT as they are usually very good coming out of there.