it appears to actually be running running multiple commands behind the scenes. I am pretty sure that is the issue.

An extremely ugly hack springs to mind

(undef,$stderr,$exit) = $ssh->cmd("command --opts > tmp.txt");
($stdout) = $ssh->cmd("cat tmp.txt");

or 

($stdout) = $ssh->cmd("command --opts > tmp.txt && cat tmp.txt");
[download]

Running this command with nohup might be worth trying as well. You may find Net::SSH2 works better.