Looks like you’ve troubleshooted the most likely causes without luck. You could try reflowing nearby FPGA pins that are on the same IO bank, especially VCCIO and GND (17,19,22). If you have a USB Blaster, you might also want to try reflashing firmware as well. Check also that Y1 outputs 27MHz signal. Problems with supplies, fw or oscillator should cause other issues as well, but those are the only reasons I can think of now in addition of very unlikely FPGA pin breakdown.