The most common reason for Upsert to miss or duplicate records is a misconfiguration of its parameters:
Primary Key (PK): The source table must have a primary key. Upon importing a table from some source systems such as MS SQL or Odata, ETL+ will map the native PK (you might need to go to ETL+ Design to review and Confirm first). Be sure to use the native PK columns, sometimes the source system documentation isn’t accurate.
Last Modified Value: It’s usually a date field. It’s common users picking the incorrect column, be sure to check the documentation and validate that column does the job as expected.