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The root of this issue was some scripts inside Drupal simply taking too long and timing out, which I believe, has been resolved by enabling e-accelerator in the site's .htaccess file. I'm hoping that has killed the errors, if it hasn't feel free to drop me a line at firstname.lastname@example.org and let me know the site is broke again :)
Special thanks to Dave at GeekISP of course for being accommodating with my silly complaints.