As I understand from your case, you’re booting from the SD card and then changing the OS using the dd command, right? Why don’t you try to boot directly with the emmc instead of changing OS? There’s a section in the BSP that describes just this process. Take a look at Section 6.3 from http://www.intel.com/content/www/us/en/embedded/products/quark/quark-x1000-bsp-build-sw-rel-user-guide.html .
Let us know if this is what you were looking for.