Thankyou @salva. Closing the out pipe worked, but adding a newline didnt. Code snippet below. 
## SEND THE QUERY FOR THE CONFIG
$message = qq~
<?xml version="1.0" encoding="UTF-8"?>
<rpc xmlns="urn:ietf:params:xml:ns:netconf:base:1.0" message-id="1">
    <get-config><source><running/></source></get-config>
</rpc>
]]>]]>~;
print $out $message;
close $out;

## PRINT THE RESULTS
while (<$in>) {
    print;
    last if $_ =~ m/\/nf:rpc-reply/;
}
close $in;
waitpid( $pid, 0 );
exit;

[download]

If I wanted to keep the $out pipe open so that further messages could be sent is there some sort of flush (I assume this is what you expected the newline to do) that could be used? I looked at the Net:OpenSSH docs in the open_ex section but dont see anything that suggests this can be done.

If this is not possible should I close and recreate the open_ex for every req/res I send?

Thanks for the prompt response, apologies if the questions are naive, perl newbie.

In reply to Re^9: SSH to remote subsystem (Net::OpenSSH?) by alrighttheresham
in thread SSH to remote subsystem (Net::OpenSSH?) by sojourner9

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