For some reason Civi is using UTC and not the Joomla time. The system, and php and mysql times are reporting correctly (Brisbane) . For Mysql I have run the following to get its time;
SELECT NOW() AS 'NOW';
For PHP I ran this
echo 'PHP date: ' . date('Y-m-d H:i:s');
Both report correct time. I also set the time zone in a local php.ini file and php is picking this up and reporting this correctly.
The error that Civi displays shows PHP as having the wrong time.
I see a timezone table in the database which is empty. Can I hardcode it in there? What else might be going on?