Problem programming EPCS device (Stratix III EP3SE110) with software

[Altera_Forum]

Hi all, 

I have been trying to program a Stratix III EP3SE110 program into the EPCS128 device on a custom board using various methods and having no luck. I have been able to program a Stratix III EP3SE260 program into its EPCS128 device on a different custom board using the flash programmer accessed from the Eclipse tool. I am using Quartus II version 11.1 SP2.  When I attempt to use the flash programmer to program the EPCS128 from the EP3SE110, I get the messages that end with:  Info: Looking for EPCS registers at address 0x01000C00 (with 32bit alignment) Info: Initial values: 00000000 00000000 00000260 00000000 00000000 00000001 Info: Valid registers found Info: EPCS signature is 0xFF Info: EPCS identifier is 0x10100C Info: No EPCS layout data - looking for section [EPCS-10100C] Info: Unable to use EPCS device Info: Leaving target processor paused Error: Error code: 8 for command: $SOPC_KIT_NIOS2/bin/nios2-flash-programmer "filename" --base=0x1000800 --epcs --sidp=0x1000020 --id=0x0 --timestamp=1381959105 --device=1 --instance=0 '--cable=USB-Blaster on localhost [USB-0]' --program --verbose --erase-all   I have also tried converting the files per the post @ http://www.alteraforum.com/forum/showthread.php?t=31375&p=127299#post127299. This does not give me any errors, but when power is cycled on the board, the software does not run although it appears that the hardware has been configured and the FPGA indicates that configuration is complete. There is no JTAG UART in the design and no UART either. The software, when run from either a command shell or the Eclipse tool, toggles 1 LED on the board off and on through a discrete from the NIOSII with 7 other LEDs turned off. After the power cycle, all 8 LEDs are either off or on with no toggling.  It appears to me that the EPCS identifier (0x10100C) is incorrect for the EPCS128, so the flash programmer does not get correct data for the device. Does anyone know how to fix that?  The other issue is that the suggested workaround of using the jic file to program the software along with the hardware is not working to run the software. Does anyone know if there is some added step required to get this to work?