Download the source code of desktop Cube from http://sourceforge.net/project/showfiles.php?group_id=91993
Compile the source code - using the provided binary will not work!!
Run a server (see normal Cube documentation) - if it says “server not responding to ping” you can either adjust your firewall settings or just use the /connect command below to play on you lan.
Within Cube iphone either: 1) menu/multiplayer/update servers, then menu/multiplayer/browse servers, or 2) menu/command and type /connect <server ip number>
If it continues to say “wrong protocol” then check that you compiled the server from source rather than using an official Cube binary.