SPI communication not working during Run time?
Sounds like a timing of events problem.   When you do that back to back spi write command are you waiting for the first one to complete?   If not when you single step the hardware probably has time to write the data out the serial bus before you write the spi register again.   

You could lazily try a delay loop between the two, but a better approach would be to check the spi status bits to see when the hardware is ready for the next write.