In VNL, bonds are only visual, they do not signify anything about the interaction between the atoms, as these are determined by the choice of calculator. I suggest you go "Properties" and increase the fuzz factor a little. Maybe this will show the bonds you are expecting?
Otherwise, please provide a python file of the configuration you got and a picture, or even better, a configuration file (f.ex. .xyz) of the configuration you expected to get.