Windows 2003 & Dos issues

We had a Novell Server and all app’s ran extremely fast. We switched to Win 2003 server and all of sudden apps are running extremely slow. Especially an old dos scheduling app. Even if we go to do a file copy from a folder on the server one time it will take an hour at other times it will take 5 minutes which is what is should take. We have check the DNS settings have installed WINS on the server all workstations are XP PRO any. There is a ISDN INternet router that is acting as a DHCP server and assigning the IP’s to the workstations. Any ideas would be appreciated.