I am experiencing an import problem with LR 6.3 & OS 10.11.2; LR does recognize the CF card on import. Prior to El Capitan, LR would sense the card and bring up the import screen; now it asks to identify the source and once the download is complete it puts the images into a "Previous Import" folder in the Catalog. In order to "Develop" the pics I have to drag/move the folder into the "Pictures" folder otherwise LR gives a "No Photos Found" error message. I am using a Mac Pro, circa 2010, and I just replaced my spindle drive with a SSD and did a fresh install of the OS but that did not correct the problem.
I think this may be a compatibility issue with El Capitan. Maybe need to wait for OSX 10.11.3?
I would suggest in the meantime creating new folder in pictures. Copying the files from the CF card to the new folder and then import into LR using “Add”