I am having the same trouble where the console does not respond when I download the file onto the board. I am trying with an example off their website- FX2_to_extsyncFIFO GPIF Single Transactions. It uses GPIF to do single word transactions. How were you able to resolve this issue?
I got it working. I had to change the default values of Code Range to 0x80-0x-0FFF and Xdata range to 0x1000 in BL51Locate tab in Options for Target.