I've recently added a few new eMacs to an Xserve-served network at our school.
When a student (belonging to a "students" group) logs in to a server-based account, the Dock contains nothing but the Finder and the Trash. This, despite the "students" group being configured so that the Dock contains a number of default applications. (I haven't checked to see if other configured preferences are being ignored.)
I had to create a number of new student accounts for the new semester. When _these_ students log in on any Mac (old or new), the Dock is properly stocked. Likewise, when the old students log in on the old Macs, things are okay.
Teachers (in the "teachers" group) logging into their accounts on old or new Macs do not experience this problem.