Does Google See Two Homepages?

Hi,

My wordpress site is installed in a subfolder which has its own index.php, there is another copy of index.php in the root folder.

I have noticed when you type the url to the root it loads the homepage and when you type the url to the subfolder it also loads the homepage. For example:

http://www.mysite.com
http://www.mysite.com/subfolder

Both load the homepage,

without

redirecting. I have lots of duplicate meta issues and I wondered if this set-up is causing search engines to see two sites?

Thanks,

T23