First time writing to EPCQ

For fresh EPCQ device you need to write the NVCR value. If you have use Quartus II programmer to write the PECQ first time this will set the NVCR value.

Then when you write the EPCQ next time without Quartus II programmer, the NVCR value still retain. Thus I believe that the reason why the configuration to FPGA was successful.

If you did not use Quartus II programmer to access fresh EPCQ device, then you need to set the NVCR by yourself. You can refer to the KDB solution link for the detail or from the EPCQ device datasheet:

https://www.altera.com/support/support-resources/knowledge-base/solutions/rd07072013_869.html