OpenOCD works fine for me if I erase the chip (so it’s running Atmel’s boot program). But as soon as I load my code and reset, the JTAG port stops working and I get lots of these messages:
Warning:value captured during scan didn’t pass the requested check: captured: 0x0f check_value: 0x01 check_mask: 0x0f
From this, I guess that I’m misconfiguring the hardware somehow and that’s causing the JTAG port not to work? 
Any suggestions?