We started implementing the latest update from WordPress today and ran into a very complicate issue with our Multisite installations. The main sites were caught in a redirect loop and would not load. After hours or diagnosis and research we came across and article that helped us resolve the issue. Thanks to our friends at Web Hosting Hero, here is the fix: http://www.webhostinghero.com/wp-multisite-stuck-in-redirect-loop/.
We recommend running through this list of items before upgrading to WordPress 3.9 if you are running Multisite to avoid any of these issues.