After upgrading from Plesk 10.3 to 10.4 for Linux (Debian 6), the update went smoothly. No error during upgradering, but there was a issue with file permissions for some of our domains on server. It seems that some Joomla sites didn't work properly due to wrong filepermission.
The issue caused the Joomla sites to either give me a error code 500 Internal Error, or error message "No configuration file found and no installation code available. Exiting...".
The fix was to change ownership on files and folders for spesific domain.
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