Does it affect my page rank or confuse Google if some of the return links are listed as http://floridaaquaticinvasivespecies.com/ and some as http://floridaaquaticinvasivespecies.com/home.asp?

The only difference being "/home.asp"?

Thanks.

Is there a reason why you want to link to http://floridaaquaticinvasivespecies.com/home.asp? page over http://floridaaquaticinvasivespecies.com

If the index page for the site has been set to home.asp and the server is handling the request correctly then it should not be a problem.