I am also fighting with my dual extruder upgrade, I am starting to wonder if it was really an upgrade afterall.
Slice3r and Repetier host seem to do whatever they want........
I am trying to print a circle with extruder 2 only, but extuder keeps wantin to print a perimiter.
Extruder temperature 2 also wants to run cooler than 1.........
Good thing I am still somewhat young..