I'm not sure I fully understand the problem, but I'll give it a shot.
It sounds like you added the Linux server to an existing NT domain with Samba and you can ping the NT domain name for the Linux server from a workstation in the same NT domain,but you can't ping the true name of the Linux server.
To be able to ping the Linux server by its true hostname you will need to have it added to DNS at your site. DNS resolves hostname to IP. This isn't needed if the machines are in the same NTdomain and you are using WINS resolution, but for any other hostname to respond it will be needed. A messy alternative is to use hosts files if you don't have DNS.
I hope this helps.