Using Windows. I edited server.cfg and placed it in Nexuiz\data, with all CTF maps defined, but when I run the server program I get...

Loaded maps/aggressor.ent

Etc. What am I doing wrong?

Did you read Nexuiz/Docs/server/readme.txt?
You have to make Nexuiz load your server.cfg. Inside the Nexuiz/Docs/server dir is a batch file for windows that will just do that. copy that batch file to Nexuiz and start that one.

Dang! It worked. Thank you. I'm gonna blame my cold for not reading the docs fully. Thanks so much!

No problem, have fun with your server and Nexuiz in general.
Would be cool to hear what kind of server this will be or if you are just playing around with it..