I had this happen, but it was on the return trip rather than the outbound. The scanner at the airport wasn't working, so the GA handwrote everyone's name and seat number on paper to get us on board. We were delayed about 2 hours so they could submit a manifest manually, and of course my miles never posted (treated as no show). I just submitted a scanned copy of my BP and bag receipts on the website and the credit was there in a few days.