Hmm.... I've had a couple of network engineers comment that what they're seeing in NCM is not the exact same config but as I'm a novice network engineer and haven't got access to the actual devices to check myself I didn't put it high on the priority list to check... if this is happening, it could be a nightmare for people using the NCM view of the config for copy/paste/edit purposes, and then pushing the resulting modified config back out to the device.
Have you checked the actually backed up config to make sure the backup process isn't b0rking the config on backup? That would be even worse