Nikon Scan NEF files

I have been using Aperature with great speed and agility. I have been able to power through several thousand images that my constantly crashing Nikon Capture batch mechanism won't handle. But when I tried to get to the files that came from my LS-4000 scanner it won't decode the file. Are there different standards from my Nikon Camera NEF than with the Scanner NEF? I checked on the Nikon site to make sure that I had the latest versions which I do. Any insight into how I might be able to get the files to read in aperature? Are there third party codecs that can be loaded into the Aperature engine?

Thanks
dmiller