Cyclone3 fails to configure

If the EPCS verification failes, you can't expect that the FPGA can be configured correctly with the EPCS data.

I see a least these possible explanations:

- the EPCS is defective (unlikely)

- you managed somehow to protect a sector of the EPCS device (would be possible with the NIOS flash programmer or when you're operating a serial flash controller in your design)

- the EPCS programming fails due to signal quality issues of the JTAG chain. This may be also caused by crosstalk of other signals (e.g. a clock) to the JTAG signals, particularly TCK.