It is a well-documented issue, but not VD's problem.
Most new DSLRS have an amazing amount of lubricants inside the mirror box. More is also thrown around by air pressure shifts due to shutter/mirror movement and the shutter/mirror hardware itself every time the shutter is tripped. It is one of the ways they assure 100,000+ activation shutter life.
Foam pads will also pick it up, but you notice it less because is diluted by the cleaning fluid on the pad.
One trick is to get a brush designed for a sub-FF sensor. It's smaller width makes accidently 'coloring outside the lines' difficult. The accepted way to do it (aside from the obvious):
1. Use a narrow brush and trim off any errant 'bristles' that decided to go off on a tangent and may touch the mirror box walls. Same as trimming errant bristles on a paint brush when painting trim.
2. Use the VD Sensor Loupe - works like a @#$R charm - spot the dust particles on the sensor. Dust stands out like craters on the moon using this sucker. No test shots required.
3. Lightly pass the charged brush JUST OVER, NOT ON the sensor where some dust was seen.
The static 'cling' on the brush will lift the dust off the sensor. Since the brush is not touching the sensor or surrounding mirror box, the odds of goop transfer to any brush threads is low.
4. Take another look with the loupe, charge the brush, and repeat in other areas where necessary.
5. If you even SUSPECT the brush as touched grease, clean it.
I can spot-clean my 1Ds2 in 2 min using this method.
And touching only the sensor is clearly what I tried to do, and I can not have been very far off the mark in doing so... yet I had these problems.
It could be with the D3, I don't know, but I understand that Visible Dust cannot be held responsible for problems with a combination of their product with another one not yet available at the time of release.