JTAG Error when Acquiring Signals in Signal Tap (STP Suddenly Stopped )

Thanks for writing back to me.

I managed to fix the issue after a lot of digging. The issue was that I hat set a load of pins to be virtual pins (4 x 32 pins). However, these pins were bi-directional, and I hadn't realised that you can't set bi-directional pins as virtual. The only thing this did was to hide the pins from me in the pin planner. In Quartus, the fitter was assigning these pins to random pins on the FPGA.

The problem was that the fitter was randomly assigning some of these bi-directional pins from my design to FPGA pins designated by the JTAG chain. So after the FPGA was programmed, these pins were reassigned and the device couldn't be seen via the JTAG.

I solved this issue by assigning the bidirectional pins in the Pin Planner to pins that I knew would not be required by the design (FMC card, LCD screen, etc)

Thanks for you help though.

Karl