Can't access JTAG chain: Stratix III dev board

Is the board still active? There should be a default configuration in the flash for the stratix that should make some leds flash when you power up the bard.

It looks indeed like a hardware issue more than software. On the development board there is a MAX chip that does the USB blaster functionnality. It is this chip that controls the JTAG signals to the Stratix. You should that the dip switches connect the right MAX pins to the Stratix JTAG ports, and it's probably best to get the right setup from the schematic rather than the documentation because there can be some mistakes in the doc.

Do you have an external USB blaster? If yes you could connect it to the board and check both the MAX chip and the Stratix (by putting the DIP switches in the correct positions to connect the external JTAG port to the correct chip).