I did a site:mysite.com and I have my .com home page plus .com/index.html the same page listed 2 times in the google search. Is this a penalty for duplicate content? How can I get rid of or fix this problem if so. It is not the domain in my profile by the way it is another site.

First, make sure all your own internal links point to example.com/ - and you can use mod_rewrite to do a 301 redirect from index.htm to the root index as example.com/