cline only works if you are changing the color of a line in a custom window. I suggest to change the cline to aline so when they join the channel it will add there nick to the corresponding color which has been designated. Also when using cline or aline you need to designate a custom windows to direct the information to fall in. Try this code to see if it is what you wanted.

Code:
on *:join:#: {
  if ($window(@Join) == $null) { //window -el @Join }
  if ($level($nick) == %CL) { aline 3 @Join $chan $nick | echo  3 $chan 0,3<CAUTION>  < $+ $nick $+ > has joined the channel  }
  if ($level($nick) == %FL) { aline 4 @Join $chan $nick | echo  4 $chan 0,4<Friend> < $+ $nick $+ > has joined $chan  }
  if ($level($nick) == %VL) { aline 6 @Join $chan $nick | echo 6 $chan 0,6<Voice> < $+ $nick $+ > has joined $chan  }
  if ($level($nick) == %OL) { aline 12 @Join $chan $nick | echo 12 $chan 0,12<Op> < $+ $nick $+ > has joined $chan  } 
}