After some experimentation on a MCDzienny server attempting to use Capture-The-Flag mode, I noticed that several of the commands are nonfunctional. This is not a new issue, as shown on this thread.
However, unlike them, I have more precise information, and pertinent error logs.
So, any use of team-management commands, excluding flag and spawn, throw errors. It appears to "Create" the team, and the team is joinable (/team join [color] does throw an error though), however when the game is started, the game mode uses the default map spawn and doesn't spawn the flags.
http://pastebin.com/m2JBE8Qa Here is a list of various errors. Unfortunately I do not have the commands that link up with them, but it should be fairly easy to match them up.