Since they exist at almost every company, I think it seems probable that it's rational. Here's a simple possible argument for their rationality:

Creating big barriers to large raises/bonuses discourages employees from sharing salary info, since there's little they can do about it. Furthermore, the more your employees are worrying about their salary, the less they're working.

It's an example of bounded rationality: http://en.wikipedia.org/wiki/Bounded_rationality

The decisions seem rational given the perspective and limitations of the decision-makers.