I don't really know what might have caused the slowdown. I'll ask around to see if any ideas come up.

I know this might be a bit tedious for you, but can you try with the latest MariaDB 5.5 and see if you get the same bad performance? You'll probably have to set-up a new datadir from the MySQL deployment.

MariaDB 5.5 should be very similar to MySQL 5.5. If we can narrow it down to a particular major version upgrade, it will be easier to track down where the slowdown happened. Probably analyzing performance logs could also hint towards a solution, but I have limited experience handling those.

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