If the 3DS is undertracked, it has some issues elsewhere. Either in 'rest of world' or last year. Nintendo has shipped 9.29 million to Other whereas VGC has it selling 10.67 million outside of the US and Japan. Now that 10.67 million would include other parts of the Americas, but I doubt they make up over 1.4 million.
The platform totals page has Europe+rest of the world at 10.03 million (with two weeks beyond the quarter). So there is some overtracking outside of Japan and the US somewhere for the 3DS.