For me the Release 1.2 Version runs with the schedules as it should
For the first, do you have a 1.2 Version? Place a schedule time on a firewall rule and then make a download of your config.xml and check if you have all needed cron items
Further Information: http://forum.pfsense.org/index.php/topic,5838.msg42769.html#msg42769
Regards
Heiko