Volcanoes exist, and aside from structures (dungeons, villages, mineshafts, etc) and weather, I haven't noticed anything else missing. I talked to the friend that set up the server last night, and he said that he just created the map with all the default settings from the server download. If I understand it right, he just ran the launch.bat file and that was it. He said there was a server config file, but he didn't mess around with it at all.
I think next time he's on, we'll have a look at the config file, and see if the structures setting was somehow flipped off I guess. And then try and generate a new map. He's very busy and I rarely see him, but I'll be sure to post back as soon as we give that a shot.