Moved from Seeking Cisco Wireless Lan Controller 5508 NCM template into the right forum.
Customer opened a ticket with support. After a number of attempts here is what we came up with that seems to work:
<Command Name="DownloadConfig" Value="show run-config"/>
<Command Name="DownloadConfigIndirect" Value="transfer upload mode ${TransferProtocol}${CRLF} transfer upload serverip ${StorageAddress}${CRLF} transfer upload filename ${StorageFilename}${CRLF}transfer upload start"/>
<Command Name="PreCommand" Value="y"/>
You will need to create a new device template and replace the download commands with above.
These commands were based off a doc we found on Cisco's website.
http://www.cisco.com/en/US/docs/wireless/controller/4.0/configuration/guide/c40mfw.html