Fancyboss

I've been trying to make a Big Dig server, and the server starts up fine and everything, and my friends can get on alright, but the world generated by the minecraft_server.jar file is vanilla. I downloaded the server straight from the site, and followed the directions, but for some reason it just gives me a vanilla world every time, yet the minimap and NEI work fine, aside from NEI not being able to spawn in any mod related items. Also, when I try to open the BigDig.jar file, it gives me a Java exception and doesn't let me extract it or run it. Any Ideas? Thanks.