I have been able to successfully run a backup-job but only manually. When I schedule a cron-job in BackWPup, I find that the job starts, but the console shows no output and stays open infinitely. No files are created and all I can to is to stop the job manually.
I'm able to reproduce this behavior.
Configuration: WordPress 3.4.2 (but now upgraded to WordPress 3.5) with BackWPup 2.1.16, hosted on byethost.
I'm willing to provide admin login to my test-environment but preferably outside of this thread.