Multisite Folder Access Suddenly Dissappeared - No Themes, Modules or Files

Ok I searched and searched but I couldn't find a similar post to this problem.

I have a multisite installation with about 8 websites.

All were running fine until this morning.

Then two sites on the multisite installation displayed very weird behaviour: Their Themes stopped showing. It was just a basic text site and basic output from Drupal.

Then I did a little more digging and found that even the files from sites/example.com/files, sites/example.com/modules and sites/example.com/themes were inaccessible via HTTP but I can still see the files via FTP.

I checked that CHMOD - file permissions and compared the files from the working websites and the non-working ones and they were identical permissions.

What's weird is that every site is setup the same way (same folder structure) and the themes for the other sites are showing but not the others.

* Multisites setup exactly the same as others which are working
* Same file permissions
* Sites setup in this structure: and setup exactly like in http://drupal.org/node/53705

drupal
    /sites
        /default
            settings.php
        /www.mysite.com
           settings.php
           /modules
           /themes
           /files

Any ideas/suggestions on where to check? I'm totally lost and I have no idea where to start looking to solve this problem.

Any help would be appreciated.

By the way - what is the correct CHMOD setting for the multisite folders? I read here that its 755 during setup and 555 after setup.