I have the same setup, and followed this guide. Thank you for it. I was having trouble with booting from the usb, then with the installed el capitan not showing as a start up option, and a few other odd things.
I was using the F5d version of BIOS, and I re-flashed the BIOS with that same version, and everything started working. I either had a corrupted BIOS or something was inadvertently set that made this not work. I did reload the optimized defaults before the re-flash, and that did not help either.
So that would be another thing to try if these directions do not work for you, is re-flash the BIOS.