You do know that any time you change from persistent connections you MUST restart Apache, right? If you don't you've failed to sever the connection from Apache to MYSQL. Leaving connections On that are supposed to be OFF will make some very very inconsistent behavior.

Other than that, if you've got something changing the username and password of the MySQL server, and or the privileges, you need to look someplace other than .threads as .threads can't change users, passwords, or flush privileges.

Cpanel or PhpMyAdmin both can. I'd start there.

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