Yep, probably so -- as the Java builds that indicates that you probably have Repast installed as Eclipse plugins, but Eclipse still doesn't know where to find the runtime classes.
I have updated the relevant page -- please see the new "installing simphony" entry:
http://www.metascapeabm.com/index.php?option=com_content&task=view&id=24&Itemid=61Please let us know if it works for you.