Here's a couple of guesses:
-Do you restart the server after changing the name? I'm pretty sure you have to.
-When creating the server, did you follow the guide on this site? If you did you would have used the below code for the "Target:". Notice it's executing 'myserver.cfg', not 'server.cfg'.
" +set dedicated 1 +set public 1 +exec myserver.cfg +map midnight"
There is probably a really easy fix if it's not those, I'm just not too experienced with servers.
Edit:
You will probably find what you need
HERE.They say just to re execute your server config file.
(In the Black Box)
"exec server.cfg"
"exec myserver.cfg"
Depending on what you have named your server config file.