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I have heard of such results on frxoops.org. There it was a site running an older version 2.0.13.2 , but yet unclear what was the vector of attack.
Which modules and versions are you using?
Avoid old notorious modules as contuedo or editors as spaw.
Check your Protector and Apache loggings for suspicious actions. Try to relate loggings with date of modified files. Follow the trail by the IP, the browser signatures and typical accesses.
Try to identify the module or script that provided entry to the malicious hacker and let us know.
Take backups and compare them to identify changed files and database tables.
Block suspected IP's their net from within Apache (.htaccess). (There is no need or benefit that the whole world should have access to your sites!)
Change all your admin passwords for XOOPS, Site admin access and MySQL and check all admin users and groups for these.
Apart from XOOPS, there can be some server vulnarabilities as well: Is directory listing switched off? Is your MySQL port closed on the servers? Is your hosting company using updated software for the servers?
I know you are a bit disappointed in XOOPS right now, but other CMS have also their share: eg to mention one: for Joomla was a major security warning just a few weeks ago.
Problem with open source is that everyone can read the source and exploit its weakness. The good news is that everyone can improve the code and learn from mistakes and we (the good guys) are with more.