When bringing in 2 stl files and running the dual wizard everything looks fine. When I hit prepare to print, one of the colored layers moves off the other one.
I had this problem too. It means you probably have the 'group and align models' option selected (bottom left corner of the Dual Extrusion Wizard dialog). This option attempts to center everything, which is often NOT what you want. If you don't want S3D to move everything around, uncheck this box.