@bplein:
So, clarification: Did all the standard cron jobs go away between Beta1 and Beta3?
No, none of the cron config entries have changed in a long time. Almost all of those are static. The filter_configure_sync one gets dynamically added or removed as needed depending on whether you're running time based rules (if you are, and that cron entry isn't there, it's added. if you aren't, and that cron entry is there, it's removed. otherwise it's left alone). The logic there looks fine after glancing over it, it's possible there are problems I'm not noticing looking through it though.