Maybe you have another Input stopping this one being triggered?
the variable %gs.ss is definetly set to %yes, this works ok for me:
Code:
on *:Input:*:{ 
  if (%gs.ss == yes) {  
    if (($1 == /msg) && (*serv iswm $2 )) || (/*serv iswm $1) {  
      if ($active != @SecureServ) { 
        echo -a ยค All $2 commands should be typed in the  $+(@,SecureServ) Window! Please type: 10/ $+ Serv      
        echo -a -    
        halt 
      }       
    }
  }
}

i changed it a little, adding the /somethingserv to be picked up on too, and removed the else, didnt really need it just the halt in the other part stops it, else its going to happen anyway.