Like the guy above says, it has to be known that FlashBios hiccups even with stock controllers.
I used my Halo Ed STOCK controller EVERY time, and the FlashBios only worked SOME of the time!
My solution? have the controller unplugged when u boot, then plug it in if you get to the part where it wants you to select your option.
It sounds janky, and is, but when I was doing my flashing FlashBios only got to the selection screen like 25% of the time, and of that percentile only 45% of the time would it let the controller work.
(Turst me it aint the controller as I spent an EASY 10 hours doing flashings.)
Happy modding!