I am having problems with several of the 3D models. The model itself looks great (for example the one below is a .stp file directly from molex) but they are not centered correctly on their pads or holes, etc and sometimes are flipped or merged.
If you use 3D models that come from the KiCad libraries, then they should fit on the footprints, or you should file a bug report for them.
If you use 3D models found somewhere on the 'net, then who knows how the’ve been made?
The models themself look OK though, there is just a bit of confusion between the step model and KiCad.
These things can be easily corrected by entering numbers in the “Rotation” and “Offset” text boxes shown in your screenshots. Jou can just rotate and move them untill they fit on the Footprint nicely.