I'm dealing with the same issue. Cyclone III stuck in POR.
All rails are present that should be present. Rail timing/sequencing is not an issue per the handbook. It just stays in Reset until all required rails are in the required ranges.
My nSTATUS line is pulled up with a 10k to 3.3V, but the chip side of the resistor is measuring to be ground.
I've looked over my design for two days since receiving my new boards. I've checked my pinout in the schematic, checked my pinout in the layout, checked for proper orientation of the chip, checked the part number of the installed chip, checked all voltage rails, etc.
I can't wait to figure this one out.
Rick