It's fixed now.You're using different folders for different profiles? I just tried it here and it worked. I need more info so I can try to recreate the issue and figure out what's going on.
This is a new feature. Once the batch has run, any new files you add to batch will automatically continue to process.The other thing with the batch manager is that after it processes all the files in the job list, the "Run" button and label beside it stay showing the "Pause" message instead of reverting back to "Run".