this might help those of you, whose server can't find the server.cfg file
While I was putting my server up, another server op came into my server and asked if an admin was around. After talking to the individual about his +exec not working, we checked the following:
1) that his command line was similar to this: "C:\Program Files\LucasArts\Star Wars JK II Jedi Outcast\GameData\jk2mp.exe" +set dedicated 2 +exec server.cfg
2) That the working directory for his server looked like this: "C:\Program Files\LucasArts\Star Wars JK II Jedi Outcast\GameData"
3) That the location of his config file was in the base dir. Example: C:\Program Files\LucasArts\Star Wars JK II Jedi Outcast\GameData\base\server.cfg
After talking to him for a bit, I found out that he had created his config file from a right-click->create->new text file. So, I had him turn off "Hide extensions for known files" in his folder options. His server.cfg file was actually named server.cfg.txt, he renamed the file to just server.cfg, and it starting working. No, I didn't flame him, I run a computer department, and we see things like this all the time.
Hopefully this will help someone else (and I put the 3 items that you should check also).