Hi there,
I’ve included the MT response here - it doesnt address what happened, and tells me to do what Id already done. The attacks affect any index & htaccess file - regardless of whether theres a CMS installed or which CMS it is.
Thanks for contacting us regarding this issue. It appears that your service was compromised as code had been injected into many parts of your account. Our engineers noticed an influx of IP addresses on the internet attempting to access your server, so we changed your Server Administrator password as a security precaution. We would recommend at this point that you consider auditing your code to make sure there have not been any changes made to it that you did not authorize. I’ve had an engineer scan and remove any malicious code or content from your scripts.
If you find anything else in your files, we recommend that you immediately remove the offending code, and do an audit of any software you might have installed (along with any plugins for that software) to make sure you are running the most current version. I’ve provided a link to our KnowledgeBase article on things to check for: http://kb.mediatemple.net/questions/1715/
If you have any other questions, or need further clarification, please let us know.