Noobes & Michael -
Not sure if you've already gotten this issue resolved but we had a similar concern with config backups on our ASA 5520, plus an additional issue.
First, the bigger annoyance to me to was that a "show running-config" on an ASA is, or at least was, paginated so copies of my downloaded config would contain a blank line ever 20-25 lines because that's were a --- more --- would have shown up if I was viewing it from the command line. Anytime we updated the config those blank lines would move around and that made the configuration change reports very difficult to read.
Second, we also noticed that the config that we had saved was not a configuration that could be loaded back into a hardware replacement device due to the lack of keys, passwords, etc.
Our solution: We changed from an SSH download of the config to a TFTP download of the config. If you're looking at the template, that's the difference between DownloadConfig and DownloadConfigIndirect. That cleared up both of the issues I mentioned above. To do that I set the following values within the node NCM connection profile properties:
Execute Scripts Using: SSH
Request Configs Using: SSH
Transfer Configs Using: TFTP
I hope that helps.
Ben