Thanks ikegami. You are right. Hmm, so my basic mistake was not to put the second pump (for reading back to $TOK_OUT). During my Internet browsing I didn't find any example with 2 pumps.

Just for the sake of curiosity. $TOK_OUT doesn't seem to be an ordinary variable. If you run the following program:

#!/usr/bin/perl -w
use IPC::Run qw(start pump finish timeout);

my $tok_program = "/bin/./cat"; 

my ($TOK_IN, $TOK_OUT, $TOK_ERR);
my $TOK = start [$tok_program], 
     '<', \$TOK_IN,
     '1>pty>',\$TOK_OUT, 
     '2>', \$TOK_ERR , 
     debug => 0 or die "Error: $?;\n"; 


while (my $line = <STDIN> ) {
    # Send input.
    $TOK_IN = $line;
    pump $TOK while length $TOK_IN;

    # Wait for output.
    pump $TOK while $TOK_OUT !~ /\n\z/;
    my $msg = $TOK_OUT;
    chomp($msg);
    print "out:$TOK_OUT;;MESSAGE=$msg;;END\n"; 

    $TOK_OUT = '';
}

finish($TOK) or die "returned: $?";
[download]

You will get:

out:1. line
;;ENDSAGE=1. line
out:2. line
;;ENDSAGE=2. line
[download]

Instead of:

out:1. line
;;MESSAGE=1. line;;END
out:2. line
;;MESAGE=2. line;;END
[download]

Do you know why?

Once more - thank you!