I'm trying to print a multi-color print with my Ultimaker 3 extended, using Cura 2.3.1 on Windows. I've designed the 3 parts using OnShape, and downloaded them as separate STL files. I can load and see the STL files, and set the print core and material type for each part. When I try to merge the 3 parts, the main part shows up in the correct location, and one of the sub-parts drops in where it should. The second sub-part comes in at the same location as the first sub-part.
I've uploaded the STL files and some screenshots to Thingiverse: