Hello Aiman,
Thanks for your response.
I have verified multiple times the pull-up and pull-down resistors on the JTAG lines.
The TCK signal is clean, crisp and not in any way noisy - but just clipped at 0.7Volts. TCK is pulled low through a 1K resistor.
I've tested with 4 cables - a mix of Altera USB Blaster 2, 1 and 3rd party tools. The actual level of the TCK signal changes depending on the cable used, with USB Blaster 2 being the best.
Pin 4 is at 1.8V, which is the VCCIO level and VCCPGM level.
All rails are as expected - the device exits reset as it is configured for active serial (via MSEL) and I can see it try and load an image from the flash device.
As a test I added a 10K pull up resistor to TCK with no download cable attached, and similarly it only goes to 0.7V.
Must be a damaged input? How can I have done this by programming with the wrong image? It really was immediate, on 2 boards, after programming with the wrong device selected. Could it have sent one of the reserved JTAG codes?
Many thanks,
Adrian