Why aren't agents moving or behaving the way they should after I change my controller's iterate method?

You may have accidentally changed the iterate method so that the following line has been removed or otherwise disabled:

super iterate.

If the controller class does not call the superclass iterate method, the simulation will not step forward in time correctly. By calling the superclass iterate method, you ensure that the "default" world stepping behavior is preserved. Every controller iterate call must include a call to "super iterate".