Not a silly question but a puzzling one. I use a D90 and Aperture and have never had a problem with NEFs. A basic check might be to try a different SD card to make sure there's no problem with the card. I presume jpegs are ok?
Next might be to delete some files (caches, plists) but I'm not enough of an expert on this to recommend exactly what. Perhaps someone else can advise?
John