I finally figured out that we had been running large databases without indexes working at all. It turns out that if I use mysqldump to dump out a database, then drop/create the database and build from the dump, none of the indexes work. Things slow to a crawl. I found inadvertantly that by issuing any "alter table" query to a table, the indexes start working again.
Is there any reason for this?
Sounds like your are using --disable-keys ( or it gets turned on implicitly) when dumping, but alter table enable keys does not happen for some reason when you restore the table. Looks like a bug in mysqldump or the server itself.
Upgrade to the latest version, if it still happens, file a bug report, and supplement your restore script with a workaround.
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