Cyril Pavillard:
Just to be more precise, all the articles on our wiki have been "erased" so we end up with hundreds of blank pages, the first time it happened I had started to manually go back from the history and restore all the pages but the content keeps being erased and this is being done over a very short time, I guess there's an automatic process doing this.
As has been pointed out, you're running a MediaWiki version that has a bug which can lead to database corruption. Upgrade to version 1.3.17, 1.4.11 or 1.5.0 ASAP to avoid serious and permanent loss of data. The 1.5.0 upgrade process is the most dangerous of all these, so make sure you have backups.
Until you do so, I suggest locking the database - if you have the necessary permissions, you should be able to do this using the page Special:Lockdb. You can also manually lock it by creating the file specified in $wgReadOnlyFile in your DefaultSettings.php.
1.5 has many security measures (rate limiting, SORBS proxy blacklist, support for spam blacklist extension etc.). Until you figure out which method is the most effective, you may want to simply disable editing by anonymous users. In 1.5, this is done with $wgGroupPermissions['*']['edit']=false; in LocalSettings.php. This will not help against a determined attacker, but may be enough to deter drive by vandalbots or spambots for some time.
HTH,
Erik