There is another caching problem as well in the build. When caching is enabled, the root blog is replaced by the first user blog. As well, the admin page uses the URL for the first user blog instead of the root blog.
Disabling the caching by uncommenting the disable_cache command on line 216 in wp-settings.php would fix this problem and the other one I had posted about earlier. Perhaps this should be done by default in the nightly builds until caching is debugged?