If you just got eXtreme, you should have downloaded the latest version, which is 2.7.
If you continue to use 2.6, make sure the upload to the server was free of errors. Download the 2.6 fixpack, and upload that too.
Only make minimal changes to server.cfg to fit your needs (name, maxclients, etc.). Do not change anything in the other configs before you made sure the server starts and you can connect to it.
Double-check the command line: make sure it has +set fs_game <your_mod_folder> +exec server.cfg +set sv_punkbuster 0 in it (where <your_mod_folder> should be replaced by the folder you installed the mod in).
For 2.7 same story, but you obviously need the 2.7 fixpack.
If you need hands-on assistance, PM me your server's FTP details.