I've a problem:
I can configurate FPGA via JTAG, when nce pulled-down with 10K, but in this case i can't configurate EPCQ-L, it says - can't recognize device ID.
When i remote the pull-down from nce - EPCQ-L can be seen and configurate. But the programm file can't reach FPGA, to download config from epcq-l to fpga i mount again pull-down.
I'd developed many board's with cyclone 3,5, max series, but this issue i can't understand.
This is weird. By right the nCE pin is meant for enabling / disabling the device. Having it pulled down is correct if you are using that FPGA for configuration.
Have you checked the signal integrity of the board? Has any of the pin affected by aggressor? Also, is this happening on all the board or certain board?