I've had this same issue since upgrading to 3.0.x. No backups run, and BackWPUp isn't visible in the network admin. Going to /wp-admin/network/admin.php?page=backwpup leads to an insufficient privileges message. Rolling back to 2.1.17 fixes the issue. It's been driving me insane for days.
After hours of digging, it doesn't seem to actually be a roles/capabilities issue, and not actually a BackWPUp problem. The culprit line for me was line 66 of backwpup.php: "if ( is_multisite() && ! is_main_site() )" The call to is_main_site() is returning false when it should be true, because the global $current_site variable doesn't have the blog_id set. It should be set to the ID of your main blog, usually 1.
Not sure yet why this is happening. But a quick workaround is to remove that conditional in backwpup.php (and the line after it), or to manually set your $current_site->blog_id to whatever your main blog ID is. Be careful: both may lead to unexpected results, and changes to a plugin file will be erased every time you upgrade the plugin.