It's hard to tell some things by your description, so here are a few items to check:
1. Make sure that on the Identification tab in Network Properties on the Win98 machines, the domain name is entered in the Workgroup box and spelled correctly.
2. Make sure that the Win98 machines are configured to log on to the domain in the properties of the Client for MS Networks and that the domain name is spelled correctly.
3. Make sure that the Client for MS Networks logon is selected as the default login - also on the Network properties page.
4. Make sure that when the login box appears, it is a Windows Networking login box and that the domain name appears and is spelled correctly.
5. Make sure that the users are spelling their user login names correctly and typing in the correct password.
If none of this works, please post again with more info - are you seeing any error messages in the event logs on your server? Can you ping by both name and IP address in both directions (ws to server and server to ws)?
Hope this helps!