Solved my own problem (fortunately!!).
Two issues were are work here.
1. So the "ICE_Debug_FLASH_DISABLE" is poorly named. I'm not using ICE at all so I thought that this didn't apply to me. A more accurate name for this field would simple be "DISABLE_FLASH_WRITE" !!
2. A resistor on the board was making the USB reset not happen. Hence it wouldn't enter bootloader mode from the main application.