>>"But SPI1_LED_CS does not go low when writing data to the SPI bus, strange enough.
--> Can you please tell us how are you testing this? Is the SPI write does not happening? Or have you seen the scope signal of the SS line?
>>"When I disconnect SPI1_DO_CS and SPI1_LED_CS from the SPI controller and control them manually it works just as expected.
So the question is if I'm missing something here?"
--> Can you please elaborate what do you mean by "control them manually"? By disconnecting do you mean are you removing the connections of wires on the pins SPI1_DO_CS and SPI1_LED_CS?
--> Have you tested SPI_Master_polling code example from the PSoC Creator Code example section? Is it working on your board? If not, can you please test it now?