Win2k issues with DOS in Netware3.2

After installing Win 2000 on a Win 98 P.C. in a Novell 3.2 network environment, I cannot run any DOS applications, while trying to run any DOS session, the following message comes up:
“All files in this directory will be deleted”
“Are you sure Y/N”
and it just hangs and I have to close the window manually. I tried to search in the Microsoft site and other sites including Brainbuzz and then I thought about writing to you. I hope you can help me out. I have checked autoexec.nt and the environment variables but could not find anything.
Hoping to hear from you soon. Happy Thanksgiving.
Meenakshi