I had this problem and solved it as follows:
I upgraded my wife's 2006 MacBook Pro (Snow Leopard) to a brand new (July 2014) MacBook Pro Retina 15". I used the migration assistant right after the initial boot of the new machine, importing everything, apps, users, settings.
Right off the bat, 2 finger scrolling did not work.
It turned out that I had to go to System Preferences and choose the ACCESSIBILITY pane, then choose "Mouse & Trackpad" from the list, then click the "Trackpad Options..." button and then click the "Scrolling" button. (I also chose the "with inertia" and set the speed to tick #3 starting from the right.) This immediately corrected the problem.
If someone said this was Windows I'd have believed it. That's just crazy. That option should be in the Trackpad preferences and it isn't.
Couldn't have solved it without other posts on this board, but I've tried to make one clear posting of the solution that worked for me. Thanks.