Hello
I read known issues and didn't find that one. On Da Vinci Duo , one fan version, I've just came across a huge problem. I was printing 2 color Vase just for a test. First raft was layed down correctly in black, few layers after, then few layers of white as color of object, than half was black half white like it should be, but then it looked like extruder was not switched correctly few layers aobove , white nozzle was printing in mid air while black one was extruding black for no reason all over the print. At next layer it was the same, black was put properly, white was not extruded , but black. Black was extruder 0, white -extruder 1. I use newest Repetier, 0.92 firmware. It was printed from SD card. Job was sliced in Cura 15.04, but it was sliced properly. All layers are like should be in this area when I checked in preview. I have this file if someone would need.
Maybe adding a few times in a row T0 or T1 commands in Cura's gcode section could solve it? I would have to check it, have no idea if it could work, anyway it would have to be put as T[n] or similar otherwise would have to be done manually. It's only a guess