Aperture can't see certain files for importing
Aperture can't see ".JPG" but can see ".jpg" and ".jpeg". I just went through a similar arduous process, name changing ".JPG" to ".jpg" and then re-importing hundreds of files; Aperture was then able to see them.

Capture 1 Pro8 was able to see both extensions; as I just wasted an hour, this has pushed me over the edge to abandon Aperture forever, which hurts, as I have used it professionally for many years. I recently updated to El Capitan, too, and this squirrelly behaviour re. these extensions started then.