Cyclone III EP3C25 High Temperature Booting Problem

You should be able to further trace down the configuration process. Does the EPCS read start, is it possibly aborted, because the FPGA means to detect a CRC error? What do you see at the CONF_DONE and nSTATUS pins?

Generally I see mainly three possible causes for configuration failure:

- FPGA isn't coming out of reset

- wrong level of configration related pins, e.g. due to leakage currents

- configuration data are considered invalid

P.S.: Also a bad solder joint or broken PCB with temperature dependant behaviour may be an explanation