You may see the following error messages in the Quartus® II software version 9.1, SP1 and SP2 when the START button is pressed for the first time to program the Encryption Key Programming (.ekp) file into a Cyclone III LS device via a USB-Blaster™ download cable.
Error: Can’t access JTAG chain
Error: Can't configure device. Expected JTAG ID code 0x******** for device 1, but found JTAG ID code 0x00000000.
Error: Operation Failed
When the START button is pressed for the second time there are no errors and the programming is successful.
This issue does not occur when using the ByteBlaster™ II or EthernetBlaster download cabels.
This is fixed in Quartus II design software version 10.0.