I'm looking at your plugin because I like the fact that active development is going on and I think it will do what I want, but I don't want to even install it given the W3 Total Cache conflict.
I saw the post where you gave instructions for a work-around when using W3Cache (Use a cron service or unix cron)
I'm testing another backup solution now which works with WP-Cron and W3 Total Cache without a problem.
Do you plan to fix the conflict between BackWPup and W3 Total Cache? If so, when? (BackWPup does look like a great plugin and I'd really like to give it a try!!)
A little bit off-topic: Does BackWPup support storing the backups in a directory on the same level as the home directory instead of in the home directory? I'd like the backups to not be accessible to the public via a web browser.