Hopefully soon after the official release of Ubuntu 12.04/Precise (in 2 weeks) we will see updated v12 TKL appliances rolled out. I would assume that the v12 Joomla appliance will have the latest stable version of Joomla included - that seems to be the way the TKL releases go. How soon after Ubuntu 12.04 release 'soon after' is though, is anybody's guess.

But whether an updated appliance will solve your problems or not, who knows... (Let's hope so).

I know nothing about Joomla (or MySQL really either...) so I'm only guessing but I suspect that the database layout may be different between the versions. My guess is that updating the DB schema has introduced (or left behind) some cruft in your DB which is triggering some sort of edge case MySQL (or Joomla) bug. My first inclination would be to do a backup of your DB and have a play in phpMyAdmin and see if there are empty records that can be deleted.

Perhaps you could approach it from another direction and create a fresh Joomla 2.5.4 instance (ie update Joomla in a clean TKL v11.3 Joomla appliance) and see if that exhibits similar behaviour (with no end user data). If not, import your DB bit by bit testing as you go so you can try to pin down the problematic parts of your DB (assuming that is the problem).