Windchill can be configured to work with SolidWorks toolbox so that it will automatically check in the toolbox component as soon as it's created for the first time in a SolidWorks session using the preference Workgroup Manager Client > Define Library Used by Application.
This works fine, but if you are using WTParts and have auto associate turned on, the WTPart that gets created for the toolbox component goes into the folder specified by the OIR or the workspace preferences, NOT in the same library as the toolbox component. See CS230149 for details.
So then someone has to find a move these Parts into the correct location.
If you are setting the Define Library Used by Application preference, then this should apply to the CAD model and the WTPart.