This has been bothering me for a while now. I just launched a brand new site and note Google has indexed the wrong damn page. I've posted the issue on Anything Digital, but seeing how several of you probably use sh404SEF, you may well be interested in the situation.
I am using the K2 CCK extension, but I doubt this would make much difference. I have only noticed this since doing more SEO on sites and using Market Samurai to track rankings, but would imagine it has been an issue for some time.
I always set up a category of "front page" for the content of the front page. sh404SEF is creating a SEF URL of
domainname.com.au/front-page/title-of-front-page. I don't use page extensions such as html or php in my setup. I am finding that Google is indexing the SEF URL instead of the domain name itself. I cannot find a way of deleting the SEF URL so that any calls on that URL are redirected to the domain name itself.
I have tried adding a redirect to cPanel, but the SEF URL still shows in the URL bar. I have also tried adding a manual Redirect 301 to the .htaccess file but it seems that sh404SEF overrides these efforts and the SEF URL still displays. The result is that Google et al would think that there is duplicate content on the site with what displays with just the domain name and what displays with the SEF URL.
Your advice on how to permanently fix this on all sites would be appreciated.