Using Study Start-Up (SSU) auto-filing and documents are not getting auto-filed into the proper binder sections.
Study Start-Up (SSU) auto-filing uses the Vault Clinical Docs method, which relies on the artifact system.
The artifact for the binder section needs to be the same artifact set in the classification of the document. This can be done by going to Admin --> Configuration --> Document Types --> [Type] --> Type Defaults.
Vault Help Documentation: Auto-Filing Documents in SSU Binders (eTMF)