Good afternoon, I assume you are referring to header JP1:
Whenever the MiniCore is reset, the operating mode is determined by the state of the SMODE pins. The MiniCore is automatically in Program Mode when the SMODE pins, which are tied together, are pulled up to +3.3 V. This happens when the MiniCore is installed on the Interface Board, and pins 1–2 on header JP1 on the Interface Board are jumpered. When the SMODE pins are pulled low by removing the jumpers from pins 1–2 on header JP1 on the Interface Board, the Rabbit 5000/6000 will operate in the Run Mode once the MiniCore is reset
JP1 pins 3-4 are reserved for future use.