Are you using the userdir mod?
In that case the thing is that PHP5 seems to be disabling running scripts from that location by default and you have to comment out the following lines:
<IfModule mod_userdir.c>
<Directory /home/*/public_html>
php_admin_flag engine Off
</Directory>
</IfModule>
in /etc/apache2/mods-enabled/php5.conf
(on a ubuntu system)