I've been having the same problem even when I have not had "Use All Controllers" selected. I have only one controller selected, and that is my Ultrastick 360.
However, I've found a solution! Deselect "Use Controllers" so that Bigbox isn't looking or any controller input, then wire the Ultrastick 360 for digital operation by connecting from the 10-wire output pin to my IPAC so that it just looks like keys pressed. I still have it connected to USB, and it's still programmable--but BigBox ignores any controller input.
