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sensei,
This sounds like some sort of control signal polarity or a power rail problem. Connecting the ByteBlaster will should put a definite value on the nCS, nCE, and nCONFIG signals that might be fixing a polarity problem. Compare you circuitry against the circuit diagram in the Device Handbook.
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I read on another post titled "Stratix II Configuration Problem" in this forum with a similar problem. The author found that disabling compressed bitstreams worked to resolve his/her issue.
I tried this on my board and now it starts up without any problems.
Problem is that I can just barely fit my design now, and I want to expand on it in the future. Does anyone have any idea WHY this would work? Seems odd to me, I mean compressed bitstreams should not affect how the programming pins are handled should it?
//TG