My comments are not expert, but ....
The A340-200 and -600 have different engines and presumably power/weight ratios, this could be a factor
The departure at JHB may have been a reduced power takeoff to save engine wear and will have been calculated - the pilots will have known the distance required to take off and this could be a factor in the time
The headwind/tailwind component on take off has an impact on the time required to break ground, this may have been a factor
The aircraft performance may have been affected by loading (we don't know what the gross weight was)
Finally, JHB is appx 5,500 feet above sea level, LHR is appx 80 feet - this wil ldefinitely have an impact on take off performance (the combination of temperature and pressure altitude is known as density altitude)
To give an example, when flying a PA28 (light single engined aircraft) out of an airfield in the LA basin (300 feet above sea level), the take off run on a 20 deg C day, calm winds, was approximately 400m.
Returning the same day, from an airport with an elevation of 6'700 feet and 14 deg C, the take off roll was at least double (I can't remember the exact numbers, it was 13 years ago.)
Obviously big aircraft dynamics will be different to tiddlers, but you get my drift?