This Knowledgebase article provides information about what to do if Neverfail Heartbeat Shutdown does not complete successfully.
A Shutdown is incomplete if it matches one of the scenarios listed below:
Scenario 1 
Neverfail exits but the NFServerR2.exe process is still visible in task manager.
The 'Exiting Now' from Neverfail dialogue box disappears as expected on Shutdown, but problems are experienced restarting the service. Check for the process 'NFServerR2.exe' in the Windows Task Manager. If the process is present, you will need to reboot the host server. After the restart, ensure the configuration is correct with either the Server Configuration wizard or the Neverfail Heartbeat Management Client.
Scenario 2 
Neverfail displays the 'Exit Now' button during service shutdown. If after waiting for shutdown to complete the 'Exit Now' button is pressed, Neverfail Heartbeat should complete shutdown.
To confirm whether the shutdown completed, check the Windows Task Manager for the NfServerR2.exe process. If the process is visible, then reboot the host server. Check the server configuration after the reboot is as expected.
Note: In either of the above cases, or if you have any other reason to suspect an unclean Shutdown, check the Windows Application and System Event Log for error messages with a source 'NFServerR2' these should state clearly whether the shutdown was successful.