Got it. If WordPress receives a request for something it has been told to look out for, it processes the request and issues redirects to keep the URL looking pretty. But if it receives a request for something it doesn't expect-- like, say, an URL bearing parameters that originated in a search engine's fevered imagination-- then it doesn't know what to do. It processes the familiar part and ignores the rest.
So then you're back with the two-part solution. One part is to tell the googlebot to ignore certain parameters. There will be a list on the "parameters" page of wmt. The other part is to forcibly redirect any request that contains a query string. Your RewriteRule will need a preceding condition looking at THE_REQUEST so you're only redirecting external queries, not internal ones.
But you will have to be very careful in your htaccess file. It already contains things WordPress put there to make the whole thing work. Make sure your additions are in the right place, where they won't conflict with anything that is already there.
And as long as you're in there, you can probably do some cleaning up. Your average CMS htaccess file is an unholy mess ;)