It's to make certain you are the person who used your entry material earlier in the day. It prevents people from sharing a ticket throughout the day or buying/selling a ticket that was used for the first half of the day. I'm guessing they probably only check for the stamp if they have a reason to question the authenticity of the ticket/parkhopper.
Also, they sometimes stamp a hand if the parks are getting crowded during the day. There are different levels of park closures and one level involves letting only people who had previously been in the park re-enter.