If this requires the official flash loader that could be a problem. I can't (or can't seem to figure out how to) use the official Espressif flash loader as I am running in Linux (ubuntu 14.04) and it doesn't seem to build or run in that environment. I'm suspecting that isn't my problem; that it is more a matter of determining the correct build parameters to generate the appropriate bin file.
I tried using gen_misc.sh to generate my binaries but that didn't seem to help.
I see that the arduino IDE for the 8266 somehow generates only 1 binary, and that binary works for both their USB download and the FOTA updates. I'm not sure how they are doing that though.
-John