If you have an instance VM running a Morpheus Agent that is successfully reporting back to Morpheus, but the Instance assigned Health Check (Monitor VM Check) is not running, then you may need to restart the Morpheus Agent service on the VM. On startup, the Morpheus Agent will register a monitor service based on the id of the check assigned to the Instance. If this check was missing when the agent was installed/started, then the monitor service will not know what check to report against. By restarting the agent you will allow it to re-start the monitor service, identify the check ID, and report into Morpheus against the check.
This was the solution for a customer facing this problem recently.