Yes, there is an issue with programming an EPCQ device with a Jam™, .jbc, or, .svf file using a 3rd party programmer.
The EPCQ devices non-volatile configuration register needs to be set correctly in order for Active Serial configuration to work. Jam, .jbc, and .svf files generated from a JTAG Indirect Configuration (.jic) file in the Quartus® II software version 13.0SP1 and earlier do not support this. This may result in configuration failure of the target FPGA.
Download the patches below for the Quartus II software version 13.0:
Download the patches below for the Quartus II software version 13.0SP1:
This issue is scheduled to be fixed in a future version of the Quartus II software.