Sorry, I only just spotted this thread!
I had to enrol biometrics on my transit in JNB (came in on a BA flight from London and left on an Air Botswana flight to Gaborone). It was pretty painless but the transit area was very quiet first thing in the morning. I had to give all ten fingerprints as well as a photo. The equipment seemed a tiny bit flaky as I kept having to lift my fingers off the scanners and put them back again to get the little lights to go green. The official seemed a little exasperated - not sure whether it was with me or the equipment! All in all it only took a couple of minutes at the desk.
On the way back I didn't have to give any biometric information so I'm not sure whether that was because I had already given it or whether the equipment wasn't working at that desk.
In between this time I actually entered and left South Africa by road at Kopfontein and no biometrics there either.