I have a SCR3310 reader and I was using Centrify Express and my CAC to log into work on Friday. I did the same thing Saturday and it randomly didn't work.
I followed the instructions to clean and uninstall everything. I restarted. My CAC reader LED flashes rapidly for 5 seconds then turns off. The reader is visible in System Report under USB, but the smart card is neither detected in Keychain Access nor in Centrify Smart Card Tool when I insert it into the card reader.
I figured it must be an issue with the firmware update on the SCR3310, so I tried updating the driver for SCR3310 as recommended by http://militarycac.org/elcapitan.htm . I still had the same error.