I could not find this problem reported so I hope I am not duplicating the report of this issue.

I have compiled both 4.1.1 and 4.1.2 with the same configuration flags that I used for 4.0.6 and now the virtual host document path is not properly recognized. I am running php as an CGI executable outside of the webserver document root, and configured it with the following flags:

./configure     --cache-file=/dev/null \
                --prefix=/usr/local \
                --enable-discard-path \
                --enable-track-vars \
                --enable-safe-mode \
                --with-exec-dir=/usr/local/php/exec/ \
                --with-pgsql=/usr/local/postgres \
                --without-mysql \
                --without-msql \
                --with-gd=/usr/local/src/gd-1.8.4 \
                --enable-gd-native-ttf \
                --with-zlib=/usr/local \
                --with-png-dir=/usr/local \
                --with-freetype-dir=/usr/local

The page that I am testing with works find if called from the main server path but not from the virtual host URL.

The following is a quick description of the Apache setup:

sandstorm.cosc.brocku.ca has docroot /www
admin.cosc.brocku.ca has docroot /www/admin

when I run the script: http://admin.cosc.brocku.ca/tools/scripts/cslookup.php 
I get and error in the php error log stating that 
/www/tools/scripts/cslookup.php can not be found when the docroot of the virtualhost should be /www/admin not /www.
I have both versions 4.1.2 and 4.0.6 on the system for testing and the same Apache configuration works with the 4.0.6 and not the 4.1.2 version of PHP.