Thank you
As is, version 1.0.X of Java SMF Backup does not work with SMF 2.0 Beta 3. This is because the action URLs have changed + some other improvements the SMF team did to the backend administration pages.
However, I've just finished some test runs of a new version I'm working on, which will also handle SMF 2.0 Beta 3. It's not yet ready to be released, so if regular backups are critical for you, please do not do the forum upgrade.
I'll post a note on the main page, as well as posting here:
http://www.simplemachines.org/community/index.php?topic=115957.0