Change the below setting in WHM > Tweak Settings to 3 (it's supposed to be a default level). Let us know if these emails persist in the same high volumes as before after the changes.

The number of times a ChkServd TCP check must fail before notification is sent and the service is restarted. On heavily loaded systems these types of service checks fail occasionaly producing erroneous indications that services are down. A setting of 0 will disable all notifications and restarts due to TCP checks. Setting this value to 3 or higher is recommended for most systems.