Probably because you have to modify the client as well.
Whenever you make changes to customize your server, you need to make the changes to the client as well or else you're going to run into issues. You can't change the server files and just assume the client will accept everything.
Let's put it this way. Don't you think it's a bit obvious that when SoE patches something in the game that your client automatically downloads it? It's patching the client files to reflect the changes made to the server.
As to what files to change, try looking on the wikki. There's also tons of info on the forums as well.
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