I know backWPup has made a ton of changes in the past 2 months and that's wreaked havoc on backups and settings. I haven't enjoyed the growing pains either.
HOWEVER, they've written a great plugin... I use on virtually every client site backing up to S3. It's the best plugin I've seen in this category.
They've worked through the problems, and most importantly, support their plugin. Kudos guys.