I’ve had two situations where we upgraded an Operations Manager 2007 SP1 environment to Operations Manager 2007 R2, and then to CU4 and had a strange situation occur it was completed. Specifically, alert volume dropped significantly after the CU4 portion of the upgrade was complete. We had completed the upgrade on all of the OpsMgr servers (including RMS, MS’ and Gateways) and had rebooted all of the OpsMgr servers. After digging into this we found that at least our custom management packs were not generating alerts after the CU4 upgrade (we validated this through manually creating events to trigger a failure). Since the OpsMgr servers had already been rebooted and the upgrades were complete concerned me. For both environments to resolve this situation we stopped all three of the System Center Operations Manager related services, renamed the “Health Service State” folder (by default stored in c:\program files\system center operations manager 2007\Health Service State) and restarted the services. After the restart of the services custom alerts began flowing properly again.
Summary: After CU4 deployment if you are not seeing custom alerts occurring you may want to rebuild the “Health Service State” folder on the RMS.