</font><font color="blue" class="small">( Why does the oil on the dip stick look clean and the oil I drained out look black? )</font>
Since I have exactly zero out of six diesels that do that, I'd say it sounds like you're using non-detergent oil. With detergent-type, contaminants small enough to pass through the filter remain suspended in the oil. With non-detergent types, they just settle out.
Either that, or you've installed a filter with a faulty or incorrect bypass for diesel.
//greg//