Remove the command mute, unless a flooding program is being used (reduce the sensibility of the automatic command block).
There is totally 0 point in blocking commands from a player. Even if muted, the server will still receive the player's command attempts, so it won't resolve a flooding problem.
So I suggest to make that the server has to receive a very large amount of commands in a certain time to detect that a player is using some software to flood the server, and in that case kick him.
Instead, if for instance, a cop is just spamming the damn cuff or arrest command, there is no point in muting him, because then he can't arrest anymore and it ruins the game for that cop.