I am using WB 4.5 and created a data set job. When i run it manually it works but its not running on the scheduled time. I tried to run it from the command prompt as well but on command prompt it looks like it ran (no error message) but my data set is not updated on the server.
What do your log files show for that dataset when executed manually, vs cmd prompt, vs scheduled?
You could also try enabling "Upload even if data hasn't changed" under your dataset "Settings" menu & see if that is the culprit.