Something

  if($input =~ /^:(\S+)!\S+ PRIVMSG (\S+) :(.*)$/i) {
     my (@test,$array_num,$reg_md5);
     @test = split(/ /,$3);
     $array_num=@test;
     for(my $i=0;$i<$array_num;$i++)
     {
        my $shifter = shift(@test);
        open(MD5LOG,">>C\:\\LOGMd5.log") || die "Failed\! : $!\n";
          print MD5LOG "$shifter\:" . md5_hex($shifter) . "\n";
        close(MD5LOG);
        dupe_check("C:\\LOGMd5.log",$shifter);
        #print "Md5 of \"$shifter\" is " . md5_hex($shifter) . "\n";
     }
  }
}

#------------#
# Sub Functs #
#------------#
sub argerror {
if($system = -1) { system(cls); } else { system(clear); }
	if(!$ARGV[0]) {
			print("\n-> You've forgotten your argument(s),\n");
			print("-> which should be the owners' nick, botnick, and server.\n");
			print("-> in that order...\n\n");
	}
}
sub dupe_check {
  open(CHECK, ">>$_[0]") || die "Error\n";
  while(my $line = <CHECK>)
  {
    if($line =~ /^$_[1].*/)
    {
      my $switch = s/$line//g;
      print CHECK $switch . "\n";
    }
  }
  close(CHECK);
}