I managed to narrow down my problem to the following issue: the subclass (the one with the @Name and @Scope annotations) keeps the values of its variables across the long running conversation, but the variables of the superclass are forgotten.

This is a snippet of my code:

public abstract class AbstractWizardController
{
        private Stack<String> pages;

        protedted void init()
        {
                pages = new Stack<String();
        }

        public void doStuff()
        {
                LOG.debug(pages);
        }
}

@Name("myWizardController")
@Scope(ScopeType.CONVERSATION)
public class WizardControllerImpl extends AbstractController
{
        public String myValue;

        @Create
        @Begin
        public void init()
        {
                super.init();
                myValue = "test";
        }

        public void doOtherStuff()
        {
                // Do other stuff here.
                LOG.debug(myValue);
        }
}

Each time I move from one page to another the doStuff() method gets called. The first time the pages Stack is an empty stack. When I move to another page the pages variable is null all of a sudden.

I recently found the solution to this problem:
1 - use getters and setters everywhere instead of referencing a class variable directly.
2 - do NOT make the getter and setter methods final.