Error: CONF_DONE failed to go high in device 1.

Ok, seems like you've used a different horizontal scaling, thus I assume the TDI signal is not only a spike but some transitions as well... If you have another board you can hook it up to the JTAG chain as second device to validate the JTAG connections are ok as the first FPGA would be in bypass when configuring the second one.. Maybe something went wrong with the layout and the signals are disturbed at the FPGA pin itself, somewhere beneath the Chip...