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Just for those who may end up with the same error. The configuration all have weak pullup resistors, and I had 10K to ground for the nCE. Changed it to ten ohms and my problem disappeared. Wish they had better comments for there error messages.
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I doubt that the explanation is right. 10k pull-down is the Altera recommended value, and I have used it in many designs without problems. I also don't think that the dedicated nCE pin has a pull-up. If Altera didn't change the Cyclone chip (rather unlikely), there's probably a short to another I/O pin (with weak pull-up) in your design or a damaged nCE input.
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