Support

Your site only uses the database prefix which is found in the configuration.php file and which you can easily see by going to Global Configuration and clicking on the Server tab. The current prefix can be found in the top right corner, next to the "Database Tables Prefix" label. This is the one and only one prefix this particular site recognises as its own. As a result, it's the one and  O N L Y   O N E  prefix Admin Tools should ever touch. If it did touch a table with another prefix it would be an immense bug.

Where the other tables come from? I have absolutely no idea. You should know. An older Joomla! installation you forgot to clean up its tables before installing / restoring your new site? Another Joomla! site sharing its database with your site? You manually restored a database backup and used the wrong prefix? I can't answer that. I can only tell you that what Admin Tools is doing is what it is supposed to do. What you want to do it would be a huge bug and should never, ever be attempted.

So it was confusing to me that your software did not amend what seemed to me relevant - particularly when my web host replied to me - when I asked a similar question - that Joomla needs the jos_files to run. I guessed that was not correct at the time but I needed some clarification.

Eek! Your host's information is two years old. Ever since Joomla! 1.7 the Joomla! installer started randomising the prefix of the database tables for security reasons (the same reasons which resulted in me adding that feature in Admin Tools about 2 1/2 years ago). So, no, the jos_ tables are not required unless your configured database table prefix is jos_. I told you how to check this. I'm under the impression that your prefix is mt7_ based on what you told me in your original post, but you'd better check this.

Thank you for the suggestions as to what might have caused this, and for the confirmation that Admin Tools would deal with everything that was relevant. I can now look into the other issues myself.

You're welcome!

But due to my naivety, could you please confirm one thing for me: that is that in a Joomla 2.5 site with my own custom prefix, no files, directories or other references should be there with a jos_ prefix?

Yes, I am 99.999% sure about that. I am leaving a 0.001% doubt just in case a braindead extension installs all of its tables with a hardcoded jos_ prefix. You know what? If you give me a list of all of your tables in your database I can quickly see if the jos_ tables are rubbish or if they fall into this 0.001% odditty.

You're welcome :)