I install xdebug from here because I am hopeless with php:
I can't guarantee that it will help you but ...
On Debian based servers here is how:
apt-get install php5-dev
tar xvfz xdebug-2.1.2.tgz
(you should get this output)
Zend Module Api No: 20090626
Zend Extension Api No: 220090626
if you don't then something is wrong - if you do then go ahead and configure.
make (< this makes xdebug.so)
cp modules/xdebug.so /usr/lib/php5/20090626
and put in this line:
zend_extension = /usr/lib/php5/20090626/xdebug.so
rm -rf xdebug-2.1.2*
Now run some php scripts and see what is going on, for example:
php -i /usr/local/ispconfig/server/cron_daily.php