Auto Detect:
Unable to scan device chain. Can't scan JTAG chain. Do you want to open the JTAG Chain Debugger to troubleshoot the JTAG chain?
JTAG Debug:
!Warning: Uncertain JTAG chain. Detected 0 device(s)
The board is programmed just the same as others, using Quartus Byteblaster. We have also swapped the FPGA on the board. The fact that the TDO serial stream matches the TDI stream would seem to indicate that those signals are passed through the FPGA as expected. This was using the JTAG debug tools of the Quartus Programmer. I am assuming that TCK making it into the FPGA as well, as I expect the TDI->TDO pass through is registered, but maybe not. All four JTAG signals can be traced and are present on the bottom side vias, leading to the dog-bone connections to the FPGA pads.