Jeff,
Try changing the Device connection template from Auto Determine, to the specific template that should be used for that device (Cisco ASA for example if this is an ASA device). If you are noticing blank lines being marked as added or removed while comparing running and startups, this might be due to the way in which NCM is downloading the configs via either SSH or Telnet.
Alternatively you could try switching the device to try and download the configs using TFTP. It would bypass the issue entirely, if this is the issue I think it is.