Is there a known problem when using an EPCQ device that has been programmed with a .POF or .JIC file that has been obtained from examining an EPCQ device using the Quartus II Programmer version 13.1?

Yes, Active Serial (AS) configuration may fail when using an EPCQ device that has been programmed with a .POF or .JIC file that has been obtained from examining an EPCQ device using the Quartus® II Programmer version 13.1.  This problem only affects EPCQ devices that are smaller than an EPCQ256. EPCQ256 devices are not affected by this problem.

The reason for this problem is that when the examine operation is performed, the programmer does not retain the correct Non Volatile Configuration Register (NVCR) value from the EPCQ device. Thus when programming an EPCQ flash device with the examined file, AS configuration will fail.

This problem is fixed in the Quartus® II software version 14.0.