Cron file names have been changed in Sun Java System Web Server 6.1. The file ns-cron.conf is called schedulerd.conf in Sun Java System Web Server 6.1, and the file cron.conf is now called scheduler.conf. These are located in the https-admserv/config directory.
Cron settings from the previous version of your Web server are however not migrated to Sun Java System Web Server 6.1during migration. Copy the cron settings for the migrated instance to the cron files.