I just posted this "user report" separately. It might address the issue, if you still have the problem, and like me you tried everything else. Good luck.
***
A user report: fixing an intermittent problem with files on CF cards failing to import, via a Lexar card reader.
I recently encountered a problem: raw files failing to import to Aperture from a Lexar CF card, via the Lexar USB 3.0 card reader, attached to my MacBook Pro retina.
Long story short: the following sequence fixed the problem.
1. Unplug card reader from MBP.
2. Insert CF card completely in card reader.
3. Plug card reader in MBP.
Lexar customer support recommended this sequence to me, when I called them for help. The very helpful person I spoke with said that Lexar has received reports of the problem with some Macs (and some Windows), but Lexar does not know the reason for the failure to import. The remedy works.