I had a similar thing happening too. If you go into machine config, viewport settings and have color by tool checked, then under the checkbox is a tool list with editable colors. NCPlot changes tool in this list everytime it reads T, or M6 so if your using a large program with many tools and you dont have enough in this list then it uses the color of unspecified tools ( just above tool list). You find when this happens the fade treats unspecified tool as one tool so thinks its the same tool. Quick fix is to put loads of tools in list.
Another problem with lathe plotting is if you have T0 or T0100 to cancel tool offset this is read as another tool change so the tool list has to cater for more tools than you actually have in your program.