I've noticed that I have to go round all the sites I use this plugin on and re-enter the Amazon S3 credentials in order to have my backups saved properly... how ridiculous!
I saw this in one of my logs as a result:
ERROR: No destination correctly defined for backup! Please correct job settings.
Presumably, though, those credentials (which really need to not be just hanging around anywhere) are still in their old place in the database?