Cron.php gives fatal error memory exhausted after update from 4.1.1 to 4.1.6

Now using civicrm with drupal 4.26. Updated drupal core from 4.25 to 4.26 and civicrm from 4.1.1 to 4.1.6. Prior to the update, civicrm cron jobs were running fine (we use civimail). Now cron.php in the browser gives
Fatal error: Allowed memory size of 33554432 bytes exhausted (tried to allocate 8192 bytes) in /sites/all/modules/civicrm/CRM/Core/BAO/OptionValue.php on line 1 (also sometimes line 116).
However the memory_limit in php.ini is 1000M. I changed it to 28M and got the same fatal error and same memory size exhausted so there's something odd going on somewhere.