I lost quite a bit of faith in DXOMark after they tested the 70-200 f/2.8 IS II and found it to be significantly worse than the v1 in terms of resolution, and refused the possibility of a subaverage sample.
Their sensor tests may still be good, though.
They said the v2 "offers slightly less resolution" but tests better on chromatic aberration. I fail to see how that qualifies as "significantly worse". Also, "These 2 lenses are very similar in term of transmission, distortion and vignetting", again hardly a condemning review.
The tests are what they are, and the results speak for themselves. Just because you're not happy with how the test turned out, or think they may have got a sub-average sample is irrelevant. The test was done with a final production sample. They put the sensor or lens through their specific testing procedures, and those are the results they got... end of story. The v1 production unit they tested was better than the v2. Sure it was probably a fluke, but if you were upgrading, there is also the possibility that your v2 could score worse than your v1. Production samples vary, it's a fact of life.
That said, I think Nikon tests better because Nikon actually uses DXOMark equipment to test their sensors, and probably uses that data to determine what's working and what's not in terms of DR, color depth, and ISO. Not that they tune their sensors to beat the test, but use the test's to determine which of their sensor designs should produce the best real world results.
In no way do I think DxO favors one brand over another, the fact that Nikon is a customer doesn't influence their DxO scores, as the scores aren't a matter of subjective bias. The scores are based on a rigid set of criteria. Nikon scores well because they use the same equipment and methods to test their sensors... then use that data to improve their sensors.