Taking wp-login.php out of the loop

I have my own custom login page. That uses another system to log the user in. I am making all the same calls that wp-login.php makes on my index page if the user is logged in via the other system. But my index page does not display the user as logged event even though they id login in the other system, and the wordpress login calls were made until the page is refreshed.

Is there any reason why the wordpress login calls are not showing the user as logged in until the page is hot a second time?

Thanks,
JB