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At first I thought this was just a damaged table, so I tried repairing via MySQL, but it appears there's more fundamental issues.

Which of the duplicates should I remove, and any further advice in dealing with this issue?

[Fri Jun 07 01:51:17 2013] [error] [client 86.42.10.69] WordPress database error Duplicate entry 'cron' for key 'option_name' for query INSERT INTO `wp_options` (`option_name`, `option_value`, `autoload`) VALUES ('cron', 'a:2:{i:1370569877;a:1:{s:16:\\"wp_version_check\\";a:1:{s:32:\\"40cd750bba9870f18aada2478b24840a\\";a:3:{s:8:\\"schedule\\";s:10:\\"twicedaily\\";s:4:\\"args\\";a:0:{}s:8:\\"interval\\";i:43200;}}}s:7:\\"version\\";i:2;}', 'yes') ON DUPLICATE KEY UPDATE `option_name` = VALUES(`option_name`), `option_value` = VALUES(`option_value`), `autoload` = VALUES(`autoload`) made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, wp_schedule_update_checks, wp_schedule_event, _set_cron_array, update_option, add_option, referer: http://www.example.com

[Fri Jun 07 01:51:17 2013] [error] [client 86.42.10.69] WordPress database error Table 'wp_options' is marked as crashed and should be repaired for query UPDATE `wp_options` SET `option_value` = 'a:2:{i:1370569877;a:2:{s:16:\\"wp_version_check\\";a:1:{s:32:\\"40cd750bba9870f18aada2478b24840a\\";a:3:{s:8:\\"schedule\\";s:10:\\"twicedaily\\";s:4:\\"args\\";a:0:{}s:8:\\"interval\\";i:43200;}}s:17:\\"wp_update_plugins\\";a:1:{s:32:\\"40cd750bba9870f18aada2478b24840a\\";a:3:{s:8:\\"schedule\\";s:10:\\"twicedaily\\";s:4:\\"args\\";a:0:{}s:8:\\"interval\\";i:43200;}}}s:7:\\"version\\";i:2;}' WHERE `option_name` = 'cron' made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, wp_schedule_update_checks, wp_schedule_event, _set_cron_array, update_option, referer: http://www.example.com
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whatever you do, now would be a good time to take a backup before changing anything ;-) I would take a look into PHPMyAdmin and check the current cron entries in wp_options. –  birgire Jun 7 '13 at 9:32
    
Aye, I have a full backup :) Will check the cron entries contents - cheers! –  AMcDermott Jun 7 '13 at 10:29
    
By "repairing via MySQL", I assume you mean you ran repair table wp_options in the command line? Or used some tool to do the same? Because that is what the second error indicates need to happen. –  s_ha_dum Jun 7 '13 at 13:24
    
I logged in and repaired this table. Later, many new errors were detected. Looks like a more fundamental issue with the server setup. –  AMcDermott Jun 11 '13 at 18:59
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