How do I get my progress notification window back?

If your jobs always run in the background and you wish to return to seeing the progress notification window appear, the most likely cause is that you have accidentally selected the

[ ] Always run in background

option at some point when the notification window was active.
To return to the default way of working simply uncheck the option

Windows->Preferences->General-> [ ] Always run in background

and the notification window should re-appear the next time you execute your job.