Just tested this as I'm currently interested in how different versions of s3d handle model files:
S3D v4.1.2 -> Seperate connected surfaces -> 3 parts
One of them (lower inner cylinder) shows problems in viewport already:
Slicing preview shows notch/cylinder starting at the same height but the lower center hole is missing.
S3D v4.0.0 -> Seperate connected surfaces -> "The selected mesh is already a single connected surface"
Slicing preview looks like the original poster mentioned, the lower cylinder starts when that "notch" part
Anybody can help me to find the reason?
Sorry if that doesn't really help you right now. But you might want to add a factory file of how you've setup
the part to print/slice so others can see exactly what's going on: "File -> Save Factory File..."
Note: I didn't do any further tests nor am I saying the model is ok/faulty. I'm just interested in how
different versions (and other slicers) handle this (the two others I've tested do properly in this case).