Programming NIOS II code to EPCQ in Quartus 13.1

You don't specifically say whether your hardware can successfully boot the FPGA from the EPCQ device. Can it? Forget Nios, just a simple rtl only project that, for example, flashes an LED.

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...after a power cycle, all pins are in tri-state...

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This implies the FPGA's isn't booting at all. So, I presume the only method you have of programming the FPGA is via JTAG. Is that right?

What method are you using to program the EPCQ device?

Is this custom hardware or a development kit?

Let me know and I will see if I can help.

Regards,

Alex