I doubt that IPv6 would help resolve the issue. Have you talked to other IT support staff at your organization or is the network and servers your responsibility? When you say “can’t see the server”, does this mean in the network browser or through ping? Is name resolution working properly for other resources on the network? Is there a firewall between you and the Windows 2003 server? Are non-Vista machines able to access this server? Have the Vista machines been added to the domain?
Doesn’t seem like there is a lot of information in your question to help troubleshoot. Can you provide more details about what troubleshooting steps you have taken and the results? Also, please provide more information about the LAN or WAN topology between the clients and the server.