I am having a same problem with the Altera Cyclone VE development board. Can you please share the hardware mods required on your board to make it work other then reprogramming the Max V and setting the MSEL switches.
I see two resistors on the EPCQ_nCS line and EPCQ_DCLK lines that need to be moved, I do not see a FET switch on this board. The resistors are moved to EPCQ side but the programmer is still failing with the message " cannot recognize silicone id for device 1."
I am using the .jic file. I tried both x1 and x4 modes. Any help or recommendations would be appreciated.