When a Job is run, it brings up a dialog that has a "Run in Background" button. In Eclipse, when this is clicked, the job progress is moved to the status line so the user can see it and bring the dialog up again. For some unknown reason, this doesn't work for us, the job will still run in the background, but the user can't get the dialog back or see progress.
The current work-around to this is to show the Progress perspective on startup, so the user can still see jobs that are running in the background.