Ghost,
My initial response would be that a small amount of black "dust" behind engine is result of oil and water being forced through the back seal of the turbo. That will dry out and splatter around the turbo and on top of the tranny. This is common in a Cummins 4BTA and 6BTA, and not viewed as a big issue. The way the turbo seals are designed, it will pass small amounts of oil and water that accumulates on the cold side of the turbo and eventually is noticed in the bottom of the turbo.
If the cold side of your turbo looks like this photo I took at the end of a season a few years back, it's a normal accumulation of oil in a Cummins turbo (per Tony Athens, Seaboard Marine, boatdiesel.com). Periodically cleaning your air filters and the turbo itself will eliminate or minimize the accumulation in the turbo. There are detailed instructions on cleaning the cold side of the turbo on boatdiesel.com.
HOWEVER... your started your thread with... "So we overhauled a Cummins 6TBA 5.9-M3", so I guess the "dust" you see could be just about anything.