I have almost the same problem, i setup the plugin and for some reason only a few files has been put on the dropbox.
And this is the backup log.
15:47:06 : Backup complete.
15:47:06 : A total of 5 files were processed.
15:47:02 : Backing up WordPress path at (/srv/http/client/public_html/).
15:47:02 : Creating SQL backup of your WordPress plugins.
15:47:02 : Creating SQL backup of your WordPress core.
15:46:47 : Backup started on Monday November 5, 2012.
Is there any way to fix this ? I LOVE this plugin, but it would be nice if it worked.