Thats a great tip. Thanks.
The post referenced is now at:
http://www.libretro.com/forums/viewtopic.php?f=2&t=201
For reference the file I needed to edit to do this was:
/opt/retropie/emulators/RetroArch/configs/USBGamepad.cfg
As explained above, your start and select codes may be different, but this is shown by the keys you have already mapped. Here is my file
input_device = "USB Gamepad "
input_driver = "udev"
input_b_btn = "2"
input_y_btn = "3"
input_select_btn = "8"
input_start_btn = "9"
input_up_axis = "-1"
input_down_axis = "+1"
input_left_axis = "-0"
input_right_axis = "+0"
input_a_btn = "1"
input_x_btn = "0"
input_l_btn = "4"
input_r_btn = "5"
input_enable_hotkey_btn = "8"
input_exit_emulator_btn = "9"