I do also have that problem after upgrading from debian lenny to squeeze that uses php 5.3.
For me the fix it has been to set error_reporting in the /etc/php5/*/php.ini files to
error_reporting = E_ALL & ~E_NOTICE & ~E_DEPRECATED
Restart apache, and then make sure the offending php.ini in /var/www/conf/web*/ picked up the settings
If it didn't make any change in the custom php.ini settings in ispconfig3 control panel and save.