You really made a big jump, upgrading from Lightroom 1 to Lightroom 5. You might do well to go to Adobe.tv or other sources and watch a few videos because Lightroom has changed dramatically. The illustration I am providing for you is from a Windows computer. But if you click on the source in the import dialog you will see a list of sources. If the card isn't listed, click on "Other" and you can locate the card using your system browser. Creating second copies is part of the options available to you in the right-hand panel of the import dialog.
If Lightroom believes you are importing from a temporary media device like a CF card or SD card, the application will only allow you to copy those files off of the device. Importing in place or "adding" directly from the card will be disabled. Your OS update probably correctly identified the nature of the device and Lightroom then respected the behavior we've had in place since Lightroom 1. I'm sorry this is interrupting your existing workflow but we have serious concerns about customers accidentally importing referenced files from a card that is subsequently reformatted in the camera. We've seen confusion around preview availability within Lightroom being mistaken for Lightroom actually "owning" the original assets.
"we have serious concerns about customers accidentally importing referenced files from a card that is subsequently reformatted in the camera"
I understand. So bury the option under the, "Only use if you really know what you are doing. You could destroy everything." heading, Or even as an external file of settings for people who know what they are doing. The point is this has forced me to take a step backward in my workflow which was already a workaround from what I really wanted. Ideally I have wanted all along:
-Import from flash card to main catalog by copy *and* a special-use link back to the flash card file for each image in the catalog
-When deleting rejected photos from the catalog, I would have a third option to delete rejected photos from the flash card.
This way, I avoid not only the new problems created by the Lightroom 5 upgrade, but I would be reducing my imports from two to one. With a slow USB connection, there were advantages in only importing by reference on the first import, but since things tend to run faster these days, I think I would come out ahead overall now.