Currently I believe that velocity is split accross both Sabre and the Old system hence the reason it doesn't work that well...
You can tell becuase the Velocity Login on the Booking Engine and the Find My Booking using Velocity Number are both components of the Sabre Frequent Flyer management solution. The old velocity website and your velocity account are all managed via the old Velocity system that was linked to Navitare and is now linked to Sabre.
I am fairly certain that they will eventually transfer all of Velocity over the Sabre as this would (hopefully) result in a more streamlined experience.
At present, car rental points allocated would be occuring with no sabre interaction (so these bits a probably still working fine), all the points from flights would presumably now be coming through Sabre (and not quite working perfectly yet).