The Columbus module from "Columbus left in orbit" scenario is invisible, either for stock Orbiter or DX9. I think something else is wrong...
Also, deleting Columbus from the line "DOCKINFO 1:0,ATV-2 2:0,ProgressM-10M 3:0,MRM1bay 4:0,Tranquility 6:0,KUboom 7:0,JEM 10:0,PMM 12:0,Soyuz-TMA21" in...