The generic IOs that share the traces with the JTAG pins are pins 28, 30, 31 of the MachXO device on the board. You should neither assign output signals to these pin locations, nor leave the software to automatically assign pins to these locations. It is suggested to lift up these 3 pins if the board fails to scan after a new pattern is programmed into the device, and after the proper programming steps in the Users Guide are followed.