The Seltrac signalling/train movement control system was installed in 1992-96, initially on the Beckton Extension and then the rest of the system cut over to it. It was before the days of formalised safety case - it just depended on the HMRI (Kit Holden, a great guy) being satisfied that the system was safe. That took quite a long time and a lot of questions were asked during the design and installation process. I recall there being a discussion on the necessary margin between civil speed (the speed that the civil/mechanical engineers stipulate the train mustn't exceed given the curvature, superelevation and height of the centre of gravity of the train, basically), what should be set as maximum speed in the automatic train protection part of the control system, and what the ATO should drive to. (The previous system had ATO as well but I think the safety calculations were redone). As I recall, it was agreed that the margins could be tighter than on a manually driven railway given that the probability of an overspeed would be lower. I have no idea what's changed, but I think that
@Peter Mugridge is probably right - somebody has done a check to a new standard. The other possibility is that the track maintenance regime is not that brilliant and that has given the safety guys the wobbles. Incidentally, changing speed limits is very easy on DLR - no signs or anything trackside involved, so changing back again would be easy too.