I recently had a KA flight, where I had to have a paper ticket. No problems with the itinerary appearing on the MPO page. And my flight ex-HKG posted miles automatically.

The return flight however, never posted. I don't know if it's because on my return I got op-up'd, but the BP did show the MPO number correctly.

My guess is that the problems are occurring because of KA integration, but only a guess.