Hi there
On the Ragnarok it is totally possible for the Button A and Button B to have been wired in backwards. The only fix I know of is to have the shop techs open up the controller and swap the wires back around. Can't "Swap" those two particular buttons in the software.
In fact you've confirmed it, if your "shut off all special mods" button is your Button B then we definitely soldered those two wires backwards! Open up a ticket on the website and they will send you the instructions to get the mod back to the shop so they can swap the wires for you.