Server. (I hope)

Yes, IPs to connect to the servers are stored in main.dll but it's probably has an encryption of some sort. But a really easy way to modify where you want to connect, even easier than tidus's way, is to go into your reg and set the ip yourself. Go to run, type in regedit and click run. Go to the following path...
HKEY_LOCAL_MACHINE > SOFTWARE > SDENTERNET > NAVYFIELDUS
Now double click on address and type in whatever you want to connect to.

Basically in the login screen, whenever you click a button, it will read from main.dll to see what IP it should store into the registry. Then whenever you start the game, it will read the IP from the registry and pre-click the server button that matches with whatever server is listed in main.dll. What you did is basically modify the server it's suppose to connect to but when you start it up, none of the servers will appear to the selected because it doesn't match the IPs in main.dll.

This is my theory and it seems very logical, go give it a try, but don't blame me if it doesn't work. :)