I’d be surprised if the form of the URL, or the place it is put is the reason. There’s probably something else wrong with the site meaning it isn’t indexed. My site uses funny urls, and is in a subdirectory, but it still comes up #1 on google for my name, and all gets indexed.
One thing I’d fix, is the front page, make it so that it is a server redirect (assuming you’re using apache, in the /.htaccess file put :
Redirect 301 /index.html http://www.ridethelakes.co.uk/cms/
) rather than a javascript redirect. Then resubmit the url to google for indexing and see if it finds the cms stuff after a bit. It may be that it isn’t finding the main page because it doesn’t follow the link from your front page.
Also, it’s probably worth putting your meta tags into joomla, rather than on the non-existent front page.
Joe