When using a Multi-Instance Keyword Type Group configured with an AutoFill Keyword Set, the AutoFill Keyword Set only expands for the first instance of the Multi-Instance Keyword Type Group when it encounters multiple instances of the primary Keyword Type on the document.
For example, the primary Keyword Type configured for an AutoFill Keyword Set is Account Number. The Account Number Keyword Value 12345 is at the beginning of every page of a document being imported. The AutoFill Keyword Set only expands for the first instance of the Account Number Keyword Value 12345. All other instances of the Multi-Keyword Type Group that exist for that document are not expanded.
For more information on AutoFill Keyword Sets, see the AutoFill Keyword Sets module reference guide.