The source is a small CSV file with something around 10 rows. I'm using a flat file connection.
The conditions are checking two string fields for different value combinations. There are three conditions total:
CreditDebit == "CREDIT" && TransCode != "750"
CreditDebit == "DEBIT"
CreditDebit == "CREDIT" && TransCode == "750"
The first two conditions are met when running via BDIS and SSIS directly, but pass no rows when run via SQL Agent. There's nothing in the source file that meets the third condition.
The account used by the SQL Agent is a dedicated Windows-integrated account. We use a Windows-integrated account because both the source and target files reside on other servers.