I have an automated job, the query pulls for instance 5 rows, but only exports 3 of them. Any idea? I'm using TDP 4.0

I have an automated, scheduled program that runs a code set, then outputs it into a xls document.
I'm having an issue where occasionally it only exports some of the rows...
if I run the query, it pulls... let's say 5 rows, but it may only export 3... or none.
but if I run the query manually it gives me 5 rows.

Any idea or suggestion?

Thank you,