Win2000Server and Dos Apps

I have a small installation, one win2000server and 10 workstations on ME and Win98. I migrated a dos accounting app from Novell over to the win2000 server then removed the novell system. The accounting app runs, but takes a long time to open and randomly seems to freeze up on different workstations. Any ideas, anything I can adjust on the server or on the workstations to fix this. Open to any ideas, I will up the points if I get a good solution Thanks