When using setCommand(String newCommand) on a CommandMinecart object, the command will be updated in the minecart's nbt (can be checked with getCommand(), /entitydata, or by activating the minecart), but when a player goes to change the command manually it will still show the old command.

When editing the minecart's command via the /entitydata command, it works correctly.

Restarting the minecraft client does not update it for the player manually editing it. Restarting the server does update it.