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Unfortunately I meet the same problem. I use EPCS16 with EP3C25F324I7. I can download sof file with JTAG and everything is OK.
I also can download pof file with AS, and verified, but the system doesn't work after reboot.
the "generate compressed bitstreams" field is unselected.
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well, to this i would first suggest to check the interconnection between EPCS and FPGA. i.e. is the ckt upto the standards of Altera, it would be nice if you could add the ckt diagram. many of the times it happens so that there is something not correct and so after bootup FPGA gets false configuration. Also how are you managing the MSEL but lines, during and after configuration?? i mean with a micro-controller or with a Jumper??
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