drn2369 yes, I have successfully flashed my custom build yocto image using the flashall script (I have never tried the ota method). Are you getting any errors during the bitbake process?
Are you able to flash a standard (non-custom) image (http://downloadmirror.intel.com/24271/eng/edison-image-ww36-14.zip) using either the flashall or ota method?