When I open a non-Chem3D file in Chem3D, the model does not look correct and/or I receive warnings in the Messages window.
Chem3D builds models according to the atom types defined in the Atom Types table. If an atom type is not defined, Chem3D will make a guess at the closest atom type available (based on carbon) in the Atom Types table. You need to define missing atom types. See the Chem3D manual on creating new atom types.
You may also need to turn off your Chem3D Building Preferences. See your manual for disabling the Building Preferences for your version of Chem3D.