This can be something very frustrating, sometimes a site can not stay updated for various reasons, though for the best help, please include the full version, like 2.5.9 or something. If you have already removed extensions as a possibility then an older version of Joomla could be the reason.
We have seen something similar on our sites before, was it on a shared server? This can happen even in a clean site on a shared server, if one account on the shared server gets hit, it could compromise the entire server. There is not much you can do about it either, nothing Joomla has can prevent such an exploit and its one reason why shared hosts can be problematic. Though this depends on the host, ones like siteground or hostgator are pretty good at keeping their infrastructure intact.
So I would recommend doing a malware scan to see what it picks up, most likely if they hit your database like that then they have a lot of files injected. Its best to restore from backup in this case and update, then malware scan.
Also look into Admin tools by akeeba, it has some useful tools to secure your site.