How closely have you looked at the LOGS? Were the sources of the files to be exported created? The expected sizes? Warnings about anything?
From your description we can't tell what size is expected for the exported files, whether you have examined them to see if they have any content, if the content is correct or short.
You may need to very closely examine all of your system settings when running the jobs. This sounds like it may be using BATCH settings which can differ from interactive sessions.
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