So I feel like a retard for asking this, but it's been bugging me enough to figure out what I've possibly messed with on the camera.
Basically my D300s will not show duplicates if I'm looking through the pictures on the camera, but as soon as I transfer the pictures to my harddrive using Nikon Transfer, I get a double of everything! For example, I'll have..._DSC1001 which will have a NEF and JPG file. Then I'll also have a _DSC1001_1 show up, duplicating both the NEF and the JPG! I just got my memory cards in the mail, so even having the ability to try to create a backup wasn't even possible.
Any thoughts?