Don't forget that they are hosting your site for free! - doesn't surprise me that they haven't responded to e-mails, as your issue requires someone to spend time looking into the problem - and when you're not paying someone to do the work... well, you'll need to wait for them to look at the issue in their own time.
The admin:Frontpage backup isn't designed to backup your whole site. - just anything you've added to the "frontpage" of the moodle site.
To back up all courses, you can use the scheduled backup service in "admin > courses > backups" but ninehub may have disabled this, as it is very heavy on server resources.
The trade-off of getting your Moodle site hosted for free may just be that you need to manually back up each course individually.
good luck!
Dan