I don't think this has to do with your classcore file, I think this has to do with your site losing it's connection to mysql.
As for your other site, are your users getting an error or what when they try to use their usertools? I looked at your source code, and it looks like you are missing a link under each of your drop-downs - something like "<script type="text/javascript"> vbmenu_register("threadtools"); </script>" (but a bit differenct for each). I would check your templates.