Thanks of the suggestion. We aleady tried running the job in 32-bit mode via the job agent.
The big picture is that we have to connect to password protected Samaba folders to retrieve files. We need to map drives(shares) with the password to resolve the connection string in the flat file connection manager. Ultimately the issue was that the batch job was mapping letter drives and as the batch file was getting reused from different developers, either the letter drives eventually ran out, or the letter drive was already mapped and the batch job failed.
The solution was to rewrite the batch file more intelligently.