Many other carriers use a "minimum fuel" flight plan (saves money) and at this time of year it is not unusual to get strong jetstreams (which always flow west to east) much further north than in the summer.
While I haven't operated from JNB from a while, (and haven't seen the very latest Meteorological data for that part of the globe) it would not be unusual at all for the flight planners to route a flight from Johannesburg to Melbourne or Sydney via Perth (or a waypoint close to it).
Nothing sinister, military or any real change, just the business of using the winds to an advantage as usual
