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I did notice I have the MSEL pins tied to 3.3V instead of 2.5V (VccA). This was copied from another design which does work to below -40C so I don't think that is what is causing my problem.
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This shouldn't be a problem, as long as the 3.3V supply comes early at power up, or at least not too much later than the 2.5V. AFAIK the MSEL pins are sampled very early in the startup process, just after the 2.5V and 1.2V supplies have come, and the pins need to have the required voltage at that time.
Can you put a scope on the EPCQ lines? That way you can find out whether the FPGA is trying to read from the flash or not (which will rule out a bad reading of the MSEL pins... or confirm it). And you can check also whether the quality of the signals themselves, you could have some glitches or bouncing on the clock that gets worse at low temperatures.
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