Seeing what appears to be same issue: 16 Macs (two MacBook Pros, iMacs, one Mac mini) upgraded to 10.11.4. On five of them, CAC loginwindow does not appear, the USB card readers LED never lights up. Middleware appears to be functioning normally. MacBook Pros were early adopters and not afflicted. CAC not seen in Keychain Access.app.
Sending "system_profiler SPUSBDataType" via ARD shows response with following:
SCR33xx v2.0 USB SC Reader:
Product ID: 0x5116
Vendor ID: 0x04e6 (Shuttle Technology)
Version: 3.04
Speed: Up to 12 Mb/sec
Manufacturer: SCM Microsystems
Location ID: 0x1d100000 / 1
Current Available (mA): 1000
Current Required (mA): 100
Extra Operating Current (mA): 0
Restarting the Mac, switching USB ports, all fail to resolve the issue. At first the failed Macs all shared the same make/model card reader, but now it doesn't appear relevant.
Submitted bugreport #25416818