I found that some of the commands I was running over ssh (from Windows to an HP-UX system) were returning early from the read loop (and terminating the command), so I had to add extra code for executing and reading the results. This was part of a larger module, but the relevant method was:

sub cmd {
  my $self = shift;
  my $cmd = shift;
  my $ssh = $self->{ssh};
  my $ch = $self->{ch};
  unless ($ch) {
     $self->{ch} = $ch = $ssh->channel;
     $ch->ext_data('merge');
     $ch->blocking(0);
     $ch->shell();
     1 while <$ch>;
  }
  print $ch "$cmd\n";
  select(undef, undef, undef, 0.2);
  print $ch "print SSH2_cmd_done\n";
  select(undef, undef, undef, 0.2);
  my @output;
  READ_LOOP: while (1) {
    local $_;
    while (<$ch>) {
      last READ_LOOP if /^SSH2_cmd_done/;
      push @output, $_;
    }
    sleep 1;
  }
  return @output;
}
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