The problem is not the control sequence

The hints at the link i provided seem to suggest it is in how you are sending the control sequences, that the timeing is very important.

Try this

use Fcntl qw/:DEFAULT/;
use IO::Termios ();
use IO::Stty ();
  use IO::Handle;
#  use IO::Socket;
  use IO::Select;

sysopen my $fh, '/dev/ttyUSB0', O_RDWR or die "sysopen: $!";
my $handle = IO::Termios->new($fh) or die "IO::Termios->new: $!";
$handle->set_mode('300,7,e,1');
IO::Stty::stty($handle, qw/ raw -parodd cs7 -cstopb parenb -ixoff -crt
+scts -hupcl -ixon -opost -onlcr -isig -icanon -iexten -echo -echoe -e
+choctl -echoke/);

my $msg1 = "\x2F\x3F\x21\x0D\x0A";
my $msg2 = "\x06\x30\x30\x30\x0D\x0A";

for my $sleep (qw /.1 .2 .3 .4 .5 .6 .7 .8 .9 1.0 1.1 1.2/) { 
  tryit ($msg1,$msg2,$sleep,2);
  } 

exit; 

sub sw{ 
  my $raw=shift; 
  $handle->syswrite($raw) == length($raw) or die "syswrite : $raw";
  } 


sub tryit { 
  my $msg1=shift; 
  my $msg2=shift; 
  my $sleep=shift; 
  my $timeout=shift; 
  my $sel_read  = IO::Select->new();
  $sel_read-> add($handle);
  my $didsomething=1; 
  my $buf; 
  print "waiting $sleep between sends\n"; 
  sw($msg1); 
  select (undef,undef,undef,$sleep); 
  sw($msg2); 
  while ($didsomething) { 
    $didsomething=0; 
    my ($rd_ptr,$wr_ptr,$er_ptr)=IO::Select->select($sel_read,undef,un
+def,$timeout);
    for my $fh (@$rd_ptr) {
      $buf=''; 
      $didsomething=1; 
      my $rv = sysread($fh, $buf, 64*1024, length($buf));
      if (!$rv) {
        if (defined($rv)) { die 'EOF';}
        else {die 'Connection terminated';}
        } # bad rv
      else { print $buf;} 
      }  # $fh 
    } # while 
  print "no chars for $timeout secs\n"; 
  } # tryit   



#for (1..300) {
#    my $toread = 1;
#    $handle->sysread(my $in, $toread)
#        == $toread or die "sysread";
#    print $in;
#}

$handle->close;
[download]

commented out last for loop

But why does it work, when I send the sequences from shell and getting it with cat?

One more guess: the two echo commands in the root node may mean the port is opened and closed twice, I think... you might try replicating that in your Perl code.

(huck's guess was a good one, too bad it didn't work...)