Program FPGA from EPCS, and boot Linux from SDCard?

The Booting and Configuration Guide touches on independent booting only briefly. I am trying to do this on a Cyclone V SOC device and am not having success.

MSEL, BSEL, CSEL lines are all good but the FPGA does not load if the BSEL is anything but 001. I am trying to load independently with the following set up:

MSEL = 10010

BSEL = 011 (NAND FLASH)

In this case the preloader and application load but the FPGA does not.

In addition, if the BSEL lines are anything but 001, I am unable load the FPGA .sof through JTAG.

Any thoughts would be appreciated.

Thanks

Kevin.