Thanks for the reply, hmm I have double and triple checked the wiring, there is no issue there as far I can tell.
Since it asks me which wire is connected where, e.g the purple D2 is connected to the chip select, it should show the chip select right? It's just odd how it's showing me the clock there in the view.
Like even if I unplug the purple wire (D2, which is supposed to be the chip select), I still see the clock moving in the view on D2. I can't tell if it's a software problem or maybe even my analog discovery 2 is broken.