Update: On December 1, 2008 Nikon USA issued a correction to the pixel pitch specification, restating it as 5.94µm - the same as the A900?. This is just getting better by the minute...
This is the first official statement that I came across regarding the Nikon D3x sensor origin (if you can trust CNET):
"Nikon officials were at pains to point out that although the D3X's sensor is manufactured in a Sony plant, it's still very much a Nikon designed sensor".
The only difference mentioned in the article is the respective pixel pitches: 5.9 microns on the A900, 5.49 microns on the D3x. If you don't know what this means - check this article about sensors and pixel pitches.