I would start by taking a look at the config spec. By default Windchill will publish everything 'As Stored'. This means whatever models were present in the workspace when the drawing was checked in are the ones that will be used when it is published. Later changes to the parts or assemblies (and checked in,) will be not visible in the drawing during publishing since the older (as stored) versions of those parts/assemblies will be used by the cad worker for publishing.
