The problem is the WLC device template that is included uses the wrong command for "DownloadConfig" in the device template.
If you go to NCM settings, under "Advanced" and "Device Templates", go make a copy of or edit your WLC template. Change the line that has
<Command Name="DownloadConfig" Value="show run-config" />
to
<Command Name="DownloadConfig" Value="show run-config commands" />
And you should be all set. This will download a real config instead of the funky stuff you're getting...
