Ok, this is straight out of a script I use frequently to setup a ssh tunnel. Replace $ssh->login() with your call to $ssh->run_ssh() or modify your script to use id/pwd auth. I haven't been able to recreate the script bombing out, so I'm not sure whether this will fix your problem or not -- speaking of which, have you made sure that you're at the current level for Net::SSH::Expect?

  #sometimes the connection isn't ready to login yet, so we try up to 
+max_retry_count times before giving up
  my $retry_count = 0;
  while(1){
    $rc = eval{$ssh->login();};
    last if defined $rc;
    last if $retry_count >= $max_retry_count;
    $retry_count++;
    sleep 1;
  }
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Now that I've looked at Expect.pm a little more closely, I can see that I'm not using $ssh->login() correctly...but it does seem to work. So give it a shot and I'll look for a better way of doing the retry loop.