I've been using libapache2-mod-auth-mysql for a CiviCRM site which requires authentication from a Drupal DB, and
it worked well generally but gave intermittent MySQL disconnections. These were making the authentication fail with an error 500, which was ... ugly ...
It took lots of digging, but eventually I found a simple patch that seems to fix the problem. It simply tells MySQL to reconnect when the link fails, which was (before MySQL 5.0) the default but isn't any more.
If this patch passes QA (gimme a week or two to be sure), I'll post updated debs for Ubuntu Feisty and Debian Etch i386 here. If you want a package sooner, just ask ... you can help me test it out :)
This is Debian bug #420010
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