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Unable to get Development App running on nFR52832_xxAA target PCB after being programed via PCA10040 Development Board, yet examples/peripheral/blinky runs OK

I have modified sdk_config.h (cii_sdk_config.h) to use xxx_CLOCK_CONFIG_LF_SRC 0 (RC not the default XTAL, as my design just uses the 32MHz Xtal)
I have modified pca10040.h (cii10040.h) to remap some of the I/O ports to match the target PCB (LED_0, etc)
I have also modified the ble_app_blinky_pca10040_s132.emProject file (ble_app_blinky_cii10040_s132.emProject) to use the cii versions of the sdk and board definition files above.

When I Build and Run using cii10040_S132 project (SEGGE Embedded Studio), it programs and verifies without error, but no LED activity, and no packets being transmitted (nRF Connect).
When I Build and Run using pca10040_S132 project (SEGGE Embedded Studio), it programs and verifies without error, LED activity is as expected, and packets being transmitted (nRF Connect) - displayed as Nordic Blinky.

Have I missed a parameter that needs to be modified?

The main,c file has been modified to compile different files for running on the PCA10040 Development Board and the target PCB

#if defined(BOARD_PCA10040) 
  #define ADVERTISING_LED                 BSP_BOARD_LED_0                       /**< Is on when device is advertising. */
  #define CONNECTED_LED                   BSP_BOARD_LED_1                       /**< Is on when device has connected. */
  #define LEDBUTTON_LED                   BSP_BOARD_LED_2                       /**< LED to be toggled with the help of the LED Button Service. */
  #define LEDBUTTON_BUTTON                BSP_BUTTON_0                          /**< Button that will trigger the notification event with the LED Button Service */
  #define DEVICE_NAME                     "Nordic_Blinky"                       /**< Name of device. Will be included in the advertising data. */
#elif defined(BOARD_CII10040)
  #define ADVERTISING_LED                 BSP_BOARD_LED_0                       /**< Is on when device is advertising. */
  #define CONNECTED_LED                   BSP_BOARD_LED_1                       /**< Is on when device has connected. */
  #define LEDBUTTON_LED                   BSP_BOARD_LED_2                       /**< LED to be toggled with the help of the LED Button Service. */
  #define LEDBUTTON_BUTTON                BSP_BUTTON_0                          /**< Button that will trigger the notification event with the LED Button Service */
  #define DEVICE_NAME                     "Antenna Test"                        /**< Name of device. Will be included in the advertising data. */
#endif
Any suggestions?
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