Did you update your context settings? Right-click the context end edit it -- then add (i.e. override) settings for the following:
- base_url
- site_url
- default_media_source
- error_page
- site_start
And a few others. See http://www.screencast.com/t/Z8EUj58vl
Do your respective index.php files initialize the proper context? Sometimes updating will revert an index file to initialize the default web context when you instead want it to initialize your custom context.
Saved my night! 