Problem:
After the automatic installation using a word press template installation wizard, you see that the permanent links have the "index.php" in the friendly url; you need to remove index.php from friendly url.
Solution:
To fix this problem you have to go to settings, permanent links, custom structure, there you will se something like this:
index.php/%year%/%month%/%day%/%postmark%/
You only need to change it like this:
/%year%/%month%/%day%/%postmark%/