Overview:
Using Study Start-Up (SSU) auto-filing and documents are not getting auto-filed into the proper binder sections.
Root Cause:
Study Start-Up (SSU) auto-filing uses the Vault Clinical Docs method, which relies on the artifact system.
Solution:
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.

Related Documentation:
Vault Help Documentation: Auto-Filing Documents in SSU Binders (eTMF)
Thank you