Gravity will pull on both balls the same. If there was nothing else in the way, it would cause both balls to accelerate at the same rate. However, there is something else in the system. There is the track, and it provides a "normal" force which pushes perpendicular to the track.
This normal force is partially opposing gravity. Near the bottom, where the track is nearly horizontal, this force is almost directly in the vertical plane, opposing gravity. Near the top, where the track is much steeper, the force isn't vertical. It's more at an angle.
To understand the movement, lets look at the situation in some funny coordinates known as curvilinear coordinates. Instead of making the x and y axes straight, we make it curved, following the track. Lets make the x axis be along the curved track, and the y axis be perpendicular to the curved track.
This is useful because it gets rid of the annoying changing normal force. Since the y axis is perpendicular to the track, we know that the normal force is always in this direction. Because its not in the x direction, along the track, the normal force can't add any velocity. We can ignore it. This is so helpful that it's worth the frustration of dealing with axes that are curved!
Which leaves us only with gravity. If the ball is very far up the track, where it is at a substantial angle, the force of gravity has a reasonable component in this x direction, along the path of the track. So a ball that starts on the top of the track accelerates forward quickly.
A ball that starts closer to the bottom of the track has gravity pulling almost in the y axis - almost perpendicular to the track. Since it has almost no acceleration in the x direction, along the track, it accelerates much more slowly.
So the ball at the bottom has to accelerate slowly to reach the end. The ball near the top gets a quick burst of acceleration early on, when the track is steep. By the time it gets to the bottom, where the acceleration is smaller, it already had enough speed to blaze through.
And, as others have pointed out, the tautochrone is a curve that is carefully designed so that these effects cancel out. The higher you start the ball, the further it has to travel, but the more it can accelerate. If you start the ball low, it doesn't have to go very far, but doesn't get to accelerate very much.