May sound mad to want this but you need it if you want Google to give you their crawl stats. I've just hacked the index page of www.propertyprophets.co.nz and have the hack documented at http://sarahk.pcpropertymanager.com/blog/genuine-404s-and-google-verification/264/
Maybe reviewing and fixing your .htaccess manually. It happened to me but using Limbo which is the flat text database equivalent for both Mambo and Joomla.
I might look at that but I would imagine I'd then have to write a plugin for every component I write and that would be a drag. This way it just looks for the option and Itemid and runs with it. Upgrades are the only issue...