Since your MEM_CS and RTC_CS pins do not have got a hardware connection (Configure-dialog) they were not connected to your multiplexor's output lines. Thus all the unneeded components were optimized-out. That happened to your status-register, look into the generated .c-file it shows that it was optimized-out.
Set the pin's properties to "Hardware Connection" and re-draw your wires, that will work
I was not aware that was occurring. I'll set them to hardware.
By the way, Do we need to invert the SS output of SPI for Active Low ICs?
Also, while I have your attention, do you know if there is any generic programming documention on Cypress. I had a bit of trouble with scope today when splitting my code fragments into their own C files with header files.
Since Cypress - C is GNU CC there is no general programming manual.
The ss-output is active-high, so you should invert the signal for an active-low device. The inversion of the component's ss signal is used to distinguish a signal from a not-multiplexed level.