It's always worth ensuring that your KF membership number has been recorded on the ticket when you check in. I fly with Virgin Australia and even if I check in online I will go to a staff member at check in or the lounge to make sure. For some reason VA's system always loses my KF number during the check in process and it has to be re-added manually by their staff. Otherwise, as you say, there can be a lot of inconvenience chasing after points.