I found some molecules in PubChem that contain a P atom, for which there is no atom type defined in CDK.
P atom types
This needs a few patches, preferably one for each atom type. I'll try to look at it asap, as this is important. Hybridization information is missing for some types, so anyone who knows a bit about phosphorus is strongly invited to add that info. I will try to make an educated guess.
First two atom types as patch:
I think the patch covered all atom types in the PDF.