After some sleuthing into why my zabbix server went down today, I realized it had to do with the housekeeper and mysql. The mysql error logs had the following:
130617 18:03:35 [Note] The following warning was suppressed 50 times during the last 33 seconds in the error log
130617 18:03:35 [Warning] Unsafe statement written to the binary log using statement format since BINLOG_FORMAT = STATEMENT. The statement is unsafe because it uses a LIMIT clause. This is unsafe because the set of rows included cannot be predicted. Statement: delete from history where itemid=215621 limit 100
I tried first disabled mysql binlogs but that didn't work. The only solution I've found is simply to disable housekeeping by setting "DisableHousekeeping=1" in the zabbix_server.conf
After setting that and restarting Zabbix it seems to be behaving normally.