Problems may occur when programming a blank EPCS device connected to a Stratix® II FPGA with a .JIC file generated in Quartus® II software version 4.2 SP1 and earlier.
The Quartus II programmer reports the following error message:
"Can't recognize silicon ID for device "
To resolve this issue, contact Altera applications to obtain patch 1.10 for Quartus II software version 4.2 SP1. This issue has been fixed in Quartus II software version 5.0 and later. This issue only affects the Stratix II family when used with active serial configuration devices.