In the Start Gcode for the Dual Extruder V2 (and, I'm guessing, all the other dual extruders) the following command:
G1 X0 Y0 Z15 F5000 ; get out the way
causes the front nozzle to hang off the bed surface. Any ooze or other filament priming of the front nozzle will spill onto the frame of the printer or the surface it is sitting on. A simple change of this line to:
G1 X0 Y50 Z15 F5000 ; get out the way
will drip onto the bed instead (change Y50 to the appropriate value for each dual extruder).
I also believe that the rear nozzle loses track of the filament position and as a result, the skirt is mostly missing. I'll investigate this issue and add to this task if I discover the cause and/or the solution.