Perhaps obviously, the wiring of the flash on the Card is set up the same as the US-style card? Thus the contents of the flash are of course NOT bit-swapped, but since the data lines are US-style on the card (I presume) the game will appear bit-swapped on a JP console. That's my guess.
gameofyou, first of all, what data line wiring did you use to the Hu connector, US-style, or JP-style?