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I would suggest exploring the new innodb storage engine instead of using MyISAM files. They are fast ACID compliant and don't suffer some of the locking issues MyISAM does.
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I missed this the first time I read this thread... But I experience several issues on my server that I suspect are related to this. I don't know mysql, however. Is this a simple fix on a per-database thing? Or will it require a major db overhault? How can I play around with this?