It Turns out that RUFUS was writing the flash drive with gpt even though it says mbr (For those who say it doesn't matter because rufus uses DD mode, I'm not sure of this after the issues I had ).
Use win32diskimager instead.
You may have to use linux to update the partition table possibly before you will see the flashdrive in windows (Disk manager showed the flashdrive but would not allow me to edit it).
I had tried 5 flash drives of different types so had to update the partition table on all of them again.
Also, I was able to boot in UEFI mode after this as well.
UPDATE: tried this again with a different version and still ran into issues so YMMV.
UPDATE UPDATE: so the last version that will work is 11.1-u7. From what I can find, the newer versions go to the USB as a GPT partition which for some reason will not UEFI boot on the machine that I have.
SpaceCadet23 got a reaction from Kered124 in FreeNAS 11.2 not booting