One thing to check is the JTAG power supply. Is it suppose to be 3.3V or 2.5V for Cyclone II? Supplying the wrong voltage can damage the JTAG port and the device as well after seeming to work initially. Also when you ohm out the JTAG pins, they may appear to be shorted to GND. If this is the case, the only soln is to replace the FPGA.
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I have similar problem too. My on-board JTAG doesn't work anymore after working for several months. I have cyclone II
i found the tck net is about 35 ohms to gnd. In both directions.
When power is supplied, I get 3.28V on TCK pin, I didn't notice over comsumption.
I can still configure with Active Serial Programming. I notice that I have no progress bar but programming is succesfull.
But I can't programm flash by Nios II.
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