Cyclone III configuration corrupts image

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I'm just trying to understand here: How could power-up conditions effect JTAG programming, many seconds after power on, but not effect programming via EPCS?

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If it was only happening on one board, you might be able to hypothesize that if say nCE was not connected, that it was 'low' enough at power on for EPCS configuration, but then floated high, so that JTAG configuration would not work.

I'll look at the schematic page.

Cheers,

Dave