Looking through the firmware I believe I should be using IO Pin 15 for the LSB of I and Pin 14 for the LSB of Q - I can see the bit toggling from the print "current GPIO state" statement but opening the captured file in a hex editor I cant see any change in the LSB of each int16 regardless of the level of pin 15/14.
I'm testing with a BasicRX daughterboard and have updated the firmware to the latest published binaries.