Custom board with epcs & cyclone error

Basically everything, but the processor works. Devices are powered correctly, the cpu is reset slightly after power on(or independently afterward) and the clock is as expected. I have seperate Jtag and epcs headers. Jtag and epcs both work to download fpga code by there respective paths. Physically the cyclone works, I can make lights blink and the clock is working fine. All in hardware though. The CPU is non-responsive through software and the flash programmer won't program the epcs through the cyclone via the jtag interface. I can program just the jtag firmware to the cyclone though.