Looking at the standings with Cavendish and Wiggins in the lead, they seemed to have changed the way the results is decided at some point. The winning pair used to be those with the most laps and the points were used when two or more teams were on the same number of laps. There was also a secondary points competition as in road stage races.
We now seem to have moved to a points based system, which is a shame as six days were traditionally centred round the Madison.