Im going to add this here because I ran in to another issue, this time with Retroarch (and because this thread comes up on google when searching)
While the controller worked for the ES menu and other port stuff I had previously configured with 360 controller mappings, the config generation script does not properly find and recognise the controller named "Afterglow Prismatic Wired Controller" and is not creating a config for it under /opt/retropie/configs/all/retroarch-joypads
so consequently, when launching an emulator (NES for example) resulted in the message in yellow saying Afterglow Prismatic Wired Controller not configured. Try as i might, it was not auto generating, and for some reason kept defaulting and regenerating configs for my LogitechF310 which wasn't even plugged in this time.
I had to get around this by manually copying an xbox360 mapping .cfg file I had previously, and replacing as follows.
[/opt/retropie/configs/all/retroarch-joypads/AfterglowPrismaticWiredController.cfg ]
input_device = "Afterglow Prismatic Wired Controller"
input_driver = "udev"
input_r_y_plus_axis = "+4"
input_l3_btn = "9"
input_r_x_minus_axis = "-3"
input_r_axis = "+5"
input_save_state_axis = "+5"
input_l2_btn = "4"
input_start_btn = "7"
input_exit_emulator_btn = "7"
input_l_y_minus_axis = "-1"
input_l_axis = "+2"
input_load_state_axis = "+2"
input_up_btn = "h0up"
input_r_y_minus_axis = "-4"
input_a_btn = "0"
input_b_btn = "1"
input_reset_btn = "1"
input_down_btn = "h0down"
input_r2_btn = "5"
input_l_x_plus_axis = "+0"
input_l_y_plus_axis = "+1"
input_r3_btn = "10"
input_right_btn = "h0right"
input_state_slot_increase_btn = "h0right"
input_x_btn = "2"
input_menu_toggle_btn = "2"
input_select_btn = "6"
input_enable_hotkey_btn = "6"
input_l_x_minus_axis = "-0"
input_y_btn = "3"
input_left_btn = "h0left"
input_state_slot_decrease_btn = "h0left"
input_r_x_plus_axis = "+3"