I had this issue too on a couple of box's. Drove me nuts till I stumbled upon the issue. Its apache's config for that domain that needs to be modified.
Open up your apache virtual domains config file which in debian is
/etc/apache2/sites-available/ispcp.conf
using your editor of choice find the domain your working on, for this Ill use one for example.com and look for the section that looks like you see below.
Code:
# httpd dmn entry cgi support END.
<Directory /var/www/virtual/example.com/htdocs>
# httpd dmn entry PHP support BEGIN.
# httpd dmn entry PHP support END.
Options -Indexes Includes FollowSymLinks MultiViews
AllowOverride All
Order allow,deny
Allow from all
</Directory>
# httpd dmn entry PHP2 support BEGIN.
<IfModule mod_php5.c>
php_admin_value open_basedir "/var/www/virtual/example.com/:/var/www/virtual/example.com/phptmp/:/usr/share/php/"
php_admin_value upload_tmp_dir "/var/www/virtual/example.com/phptmp/"
php_admin_value session.save_path "/var/www/virtual/example.com/phptmp/"
php_admin_value sendmail_path '/usr/sbin/sendmail -f vu5150 -t -i'
</IfModule>
<IfModule mod_fastcgi.c>
ScriptAlias /php5/ /var/www/fcgi/example.com/
<Directory "/var/www/fcgi/example.com">
AllowOverride All
Options +ExecCGI -MultiViews -Indexes
Order allow,deny
Allow from all
</Directory>
</IfModule>
There is two things I have changed to make it work, both same directive.
Look for the lines AllowOverride. By default they are set in these two sections to None. Change it to All and restart apache. That should resolve your issue and you'll get SEF urls again.
HTH.
:cool:Tnt