Odd Homepage Question (index.php optimsed, domain.com not)

I have a new client that has a site which I've optimised the on-page on the whole site. However, the homepage is being a problem...When you click on the 'home' button it is just domain.com but the page I've optimised is domain.com/index.php and there is a domain.com/home, which isn't optimised. It's almost as if the 'home' button swaps between all three pages, in a random way.

I have tried to 301 the pages so only domain.com shows up, but I got a redirect loop when I did that. It's really frustrating but I'm sure it's a simple solution, this sort of stuff isn't my strong point and his web developer knows even less than I do!!

wordpress ? htaccess checked ?

Not wordpress. Not sure what you mean by htaccess checked? I have 301d the non-www to the www domain, but don't understand why the /index.php is optimised to my requirements while the / and /home aren't...it's weird. It's not pulling the data from the index.php file and therefore has three exactly the same homepages.

Anyone got any other ideas/help?