I've just had the same experience.
Miles for LHR-JNB appeared after the usual interval, but JNB-LHR still to post 5days later. When I tried the "claim missing miles" doobry on the Skywards website, it told me my ticket number was invalid!
Have tried to email route, but will call if I havent heard back after a week (I'm not generally a fan of calling in. I spend half the call trying to decipher what has just been said over background noise. Think my ears are on the way out. Too much loud music.)