If your WP site is hosted on a windows server and you want to upgrade to the 3.1 you might end up a redirect loop error while attempting to access your site homepage after the upgrade is completed. However you can get to the WP back-end with no issue. Even if you try to install a fresh 3.1 on a windows server you will face the same problem.

All pages that have /index.php at the beginning of their permalinks come up with no problem means that the post pages if permalink is set in such a way that the /index.php is at the beginning of it would be accessible.

Deactivating all plugins, switching to Word Press 3.1 default theme won’t fix the issue because this is not a theme-related or plugin-related problem.  Even altering the permalink structure would not resolve it. Clearing the browser cookies also won’t fix it.

This is known as canonical redirect issue that would result in too many redirects (better to say infinite redirect) in windows platforms.

The quick fix would be disabling the “canonical URL redirect” feature which can be done either by installing the “XO Permalink Fix & Disable Canonical Redirects Pack” plugin or by adding the following code to the function.php file of your current theme:

remove_filter('template_redirect', 'redirect_canonical')