I have noticed that when I initialise SPI with SPI.begin() the D13 LED does not work anymore even though I am not using SPI at the time of trying to blink the LED. Does anyone know why that is?
The system led is connected to D13, and D13 is part of the SPI bus.
After you called SPI.begin(), D13 is controlled by the SPI hardware inside the microcontroller.
Ah OK I see, thanks.