You may experience intermittent lockup or failures during JIC programming and verification when using the EthernetBlaster II download cable. You may also experience very slow operation during Stratix® II device non-volatile key programming.
To fix the issue, you have to upgrade to the latest firmware (Firmware 519_179). You can get the latest firmware at EthernetBlaster II Firmware Upgrade. The update can be done from the EthernetBlaster II download cable GUI in the Upgrade Firmware tab.