Why does the Quartus II programmer generate JTAG error messages when programming a design security key using Encryption Key Programming (.ekp) into a Cyclone III LS device via a USB-Blaster?

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.