Custom board with epcs & cyclone error

Not clear on what does or doesn't work on your board.

I assume you have verified the devices are powered within spec, reset lines OK, and the master clock is present and clean.

Do you have both a Jtag header and a header for the Epcs device?

If so, can you program the Epcs device with active serial mode using its header?

If not, are the data&clock signals to the device present and clean?

Are the Jtag data&clock signals present and clean?

Some serial bus designs benefit from adding small series resistors on these lines.

Our custom board uses a cyclone with an Epcs1, but no configuration controller such as the kit board.

I can program the Epcs via its header, and I can also use the Jtag header to run applications, configure the FPGA,

and program flash using the flash programmer utility. What I cannot do (yet) is program the Epcs with the flash utility.