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I've had this happen before on some client sites. With Joomla, you have to keep it 100% up to date (including any mods you add to it) as security patches are released or you will most assuredly get hacked at some point. Also, I would not be surprised if you have some files they uploaded sitting on your server so check every file/folder by date and look for new files you do not recognize.
If you rebuild, you may want to look into using Wordpress as a CMS.
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