I had also problems with the Zend optimzer which worked only over the apache webserver somehow, so I used this command in my cron table which it runs every 2 minutes with batch processing enabled:

Without htaccess protection:
Code:
wget -q http://example.de/cron.php & rm -f ./cron.php*

With htaccess protection:
Code:
wget -q --http-user=admin --http-password=ddf33example http://example.de/cron.php & rm -f ./cron.php*