I just tested your plug-in and it seems to be doing what I would expect. Though I can't use it, because compression of the backup files appears to be mandatory. Unfortunately my hoster does not support mod_gzip or mod_deflate. This causes the backup jobs to run indefinitely. I don't mind, because I will move to another hoster anyway, but others might have the same problem. So you might want to consider making compression an option.
The other thing I noticed concerns the user interface which appears to be complex, although it's actually well structured. It would be cool if you could make the many choices for backup destinations collapsable - and/or the boxes movable. In the end, most users will only use one, but have to scroll through a long list of unused options.
Okay, I will try BackWPup again once I have moved my site to a new hoster. Thanks for developing this plug-in!