I have a Taz 5 that I just installed the dual extruder for.
Part of the process is calibrating the extruder to let a slicer know what the distance between the nozzles are in X and Y. After calibration, my numbers are -.06 for x and -51.79 for Y. I entered this data into Slic3r and the calibration box printed out perfectly.
I setup a two color model in S3D which consisted of two STL's each with a different process and different extruder. In the second process (for the second extruder) I entered an offset in the Gcode tab of -06 x and 51.79 for y (S3D reverses the Y axis in comparison to Slic3r). When printing, I noticed a gap in Y that was bigger than any error you might expect, but small enough to know the offsets I entered were the correct sign. They were "in the neighborhood" of being correct, but were wrong.
Long story short, I ended up having to enter -.3 for x and 53.8 for y. a full 2mm difference!
With calipers my nozzles are 51.8 mm apart in Y (center to center of nozzles)
I double checked my stl's and they are lined up perfectly in S3D. I've attached the factory file and gcode (zip file) for reference.
So what am I doing wrong? Or is there a bug in S3d?