A bit of a late reply, but here goes:
Downloading a file manually uses one profile (let's call it the manual profile), while executing a job uses another profile (let's call that one the Scheduler profile). Even though the two profiles are the same name, connect to the same site, etc., configuring rename rules in one does not create them in the other. The simple fix? delete your existing Scheduler profile, right click your manual profile, and select "Copy to Scheduler." This will create a new Scheduler job with the exact same config as your manual job, including rename rules.