When I change my oil & filter, it will stay clear for 500 miles, then turn black from 500 to 1000. This is both with EGR and now with it blocked.
I notice you can get a bit more oil out of these engines if you let them drain long enough. An oil change takes the better part of 40 minutes for me. Start it draining, come back in 15, pull the filter, come back in 20, new filter, drain plug back in, fill it up.
My Dad has a '99 Cummins, and that oil is black by the time it hits the pan. You don't even have to start the engine. Just fill it up and check the stick: yep, black! My old '82 6.2L is the same way.
I suspect it has a lot to do with the oil you use, and how much soot makes it into the oil. Perhaps some soot builds up between changes as well.