When gravity is doing the work, the acceleration is independent of mass. That is, heavier trains do not go faster than lighter ones. Heavier trains have more total energy, but because of the added mass, they don't accelerate any faster.
When you launch a coaster, though, the amount of force you apply will be related to the mass of the train and the speed you want to achieve. So if you apply a given amount of force to the train, the speed it reaches will vary with the train's mass. Then the train will start up the spike, and gravity will drag it back down, accelerating it at a constant rate; when its velocity reaches zero, it will start to fall back down the tower. The distance the train goes up the tower will depend on how fast the train is going when gravity takes over.
Since a lighter train has less mass to move, for a given amount of energy applied to the train, the lighter train will go faster, and thus, go higher up the tower.
--Dave Althoff, Jr.