Re: Burnt FPGA?
If the FPGA bit file has outputs defined on physical pins that are tied high or low, aka VCC or GND, there will be a bus contention which will cause the device to overheat. If enough of these IOBs are loaded like this, it could damage the FPGA.
I would take a failed board and a new board and compare the resistance readings across all power supply pins connected to the device. If the bad FPGA was fried internally, then you will see the difference on the resistance checks.
Are you 100% sure you are loading the proper bit file? You would think that these bit files are error checked by the FPGA, but not really. Several years ago, we had a situation where an FPGA would get extremely hot after incircuit reprogramming. It was finally determined that due to a software error, the FPGA was being loaded with a bit file for a cross-bar switch part that was also on the board. Wrong bit file can mean massive heat.
I would suggest generating a very simple design with only one output that flashed an LED, or toggle a single output pin. Load this extremely limited design into the parts and verify that it works. This will prove out your boards and JTAG cable. Once this is working, go back and start debugging the full design.
Finally, are you sure the FPGAs can from Altera? We have had vendors try to slip us "gray market" Xilinx FPGAs. These are either factory rejects that have been smuggled out of the fabs, or sometimes direct fakes. After fighting many weird problems, we now demand that the board assemblers buy FPGAs and CPLDs only from our approved distributor.