[wp-hackers] permalinks with pathinfo

[IC IC]

With a new godady windows account, and with a fresh installation of
wordpress with no plugins activated, I am having the following issue.

When I go to the permalinks screen, I get to see this

Day and name    http://mysite.com/index.php/2011/11/22/sample-post/
Month and name    http://mysite.com/index.php/2011/11/sample-post/

as opposed to this;

Day and name    http://mysite.com//2011/11/22/sample-post/
Month and name    http://mysite.com/2011/11/sample-post/

Obviously, that index.php in the middle is not my choice. The question how
did it get there? It doe not appear with my other wordpress/godaddy sites.

If I click on the "day and name" common settings option for exammple, the
custom structure is populated as
/index.php/%year%/%monthnum%/%day%/%postname%/

and when I save those changes, ( thoug I do not want that structure), the
site works;  all permalinks are updated to work with the name structure. so
my contactus page becomes http://mysite.com/contactus instead of the
page_id=3

When I select custom structure and make it /%postname%/ ( as I wanted) , I
end up getting the permalinks to be updated as I like except that I end up
404s on all urls. When I insert the index.php in the middle on a 404 URL,
wordpress is able to find the page.

Any insight in this matter is appreciated.