Alert Lags

We are having intermittent issues with alerts and polling.

For example a server went down, which was running tomcat, db2 and snmp. The first monitor to alert was a http-url sequence. Then about 30 minutes later snmp alerted, then 60 minutes later tomcat alerted, then another hour db2 alerted and then in another hour the server alerted.

When the issue was finally resolved we still have monitors that are lagging to report they are clear. Additionally their next poll values are in the past?

What is happening? Build is 6600. The only thing I can think of is that I've enabled ports to test in the availability config file.