Aperture 2 won't recognize jpg files on Canon S90 after upgrading to 10.6.3

It says there are no files to import, when in fact there are many. I have tested camera on a friends computer and the files imported perfectly (using iPhoto). Could the OS upgrade have anything to do with it? Any ideas? Thanks!

You didn't mention which camera's NEF files you were referring to.  This is important because each camera's raw file formats are different.
If it's a for a Nikon that's come out in the past year or so, Aperture 2.14 won't be able to read it - you'll need Aperture 3.
Which camera are the NEFs from?

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