Unable to Program EPCS16 in system

[Altera_Forum]

I recently designed and put together my first FPGA board. I can configure the FPGA over JTAG fine, but the EEPROM seems out of reach. If I use the USB-Blaster in AS mode, it fails to get the device ID, and if I use a .jic file, the process fails, with no explanation. Other than that, the board behaves as desired (so far). 

 I'm using an EP4CE22E22C8N with an EPCS16 flash chip. They are configured as shown in the Cyclone-IV Handbook on pp. 218. I can configure the FPGA over JTAG, however I cannot configure the EPCS16 over JTAG or the AS header. I've attached the configuration page from my schematic.  Thanks for any help.

[Altera_Forum]

Why did You choose setup as in Figure 8–28, rather than as in Figure 8–29 which is more convenient, requires less BOM, and besides all, requires only one 2x5 pin connector ( only for JTAG ).

[Altera_Forum]

--- Quote Start ---  Why did You choose setup as in Figure 8–28, rather than as in Figure 8–29 which is more convenient, requires less BOM, and besides all, requires only one 2x5 pin connector ( only for JTAG ).  --- Quote End ---    It's mostly a learning experience for me. I was going to say so I could use the design encryption, but then when I went to check that I found that's not an option for the Cyclone IV. I've been messing around with the DE0-Nano, and wanted to try doing my own board.

[Altera_Forum]

--- Quote Start ---   I can configure the FPGA over JTAG, however I cannot configure the EPCS16 over JTAG or the AS header.  --- Quote End ---   As far as I know EPCS16 over JTAG can be programmed only in the setup according to Figure 8–29 and its very convenient.  If setup is according to Figure 8–28, then You can only program EPCS16 through AS Mode using appropriate 2x5 pin header. Maybe someone else would help You with AS Mode. I never studied or used it ....

[Altera_Forum]

Fixed it. It was the protection diodes. They were in backwards (idiot). The EEPROM now programs correctly both with a .jic file and a .pof file using the appropriate header for each.

[Altera_Forum]

Glad you found your problem. Both methods work. We tend to use Active Serial as you are doing, or use passive serial or passive parallel modes, if we have a CPU that has the flash storage to hold the bitfile. 

 They all work. Everyone has their preference. We tend to not install the headers in production and use a bed of nails approach. If the header sizes are a problem, we have used custom headers as well, with a breakout board, or bed of nails setup to access them.  Regards,  Pete