Policies

I have nt 4.0 server and thier has been some policies put in place. config.pol for the win 98 clients and ntconfig.pol for the windows 2000 pro clients. The technician isn’t sure if the win 2000 are reading the ntconfig policies or if it is reading both or if win2000 will even read polcies from a NT server. We have a lot of problems with outlook setting sticking and user folders being emptied . It recreates user app folder,cookies,history,and others when they login but not always any ideas?