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I was seeing intermittent errors using this module against MySQL 5.0 on both Debian Etch and Ubuntu Feisty. It happens due to a changed behaviour (the default is not to reconnect() when the connection drops from MySQL 5.0.3+) and needs a small patch to the libapache-mod-auth-mysql or libapache2-mod-auth-mysql source. The patch is available at Giant Robot and the Debian bug is #420010
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