I posted a problem regarding not being able to switch off Theme designer mode after upgrading from Moodle 2.2 to moodle 2.3. (see my post earlier this week: http://moodle.org/mod/forum/discuss.php?d=212192
Our main moodle installation dates back through all upgrades to 2004, so to try and find out what happened I tested it on a fresh install that was upgraded from 2.1 through 2.2 to 2.3. In the move from 2.2 to 2.3 the system advises to change the database from MyISAM to InnoDB.
This I did, using the built in moodle script - then updated cvs to the latest 2.3 version and immediately the theme was lost and no theme shows correctly at all without turning Theme designer mode on.